Header list of 1gm1.pdb file
Complete list - r 28 2 Bytes
HEADER HYDROLASE 06-SEP-01 1GM1
TITLE SECOND PDZ DOMAIN (PDZ2) OF PTP-BL
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN TYROSINE PHOSPHATASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PDZ2;
COMPND 5 SYNONYM: NONRECEPTOR-TYPE, 13, PROTEIN-TYROSINE PHOSPHATASE RIP,
COMPND 6 PHOSPHOPROTEIN PHOSPHATASE, PROTEIN-TYROSINE-PHOSPHATASE,
COMPND 7 PHOSPHOTYROSINE PHOSPHATASE, PTPASE, PTP36, BAS-LIKE;
COMPND 8 EC: 3.1.3.48;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS PDZ, PTP-BL, FAS INTERACTION, LIM INTERACTION, STRUCTURAL PROTEIN,
KEYWDS 2 CYTOSKELETON, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 35
AUTHOR T.WALMA,M.TESSARI,J.AELEN,J.SCHEPENS,W.HENDRIKS,G.W.VUISTER
REVDAT 3 28-MAR-18 1GM1 1 SOURCE JRNL
REVDAT 2 24-FEB-09 1GM1 1 VERSN
REVDAT 1 08-MAR-02 1GM1 0
JRNL AUTH T.WALMA,C.A.SPRONK,M.TESSARI,J.AELEN,J.SCHEPENS,W.HENDRIKS,
JRNL AUTH 2 G.W.VUISTER
JRNL TITL STRUCTURE, DYNAMICS AND BINDING CHARACTERISTICS OF THE
JRNL TITL 2 SECOND PDZ DOMAIN OF PTP-BL.
JRNL REF J. MOL. BIOL. V. 316 1101 2002
JRNL REFN ISSN 0022-2836
JRNL PMID 11884147
JRNL DOI 10.1006/JMBI.2002.5402
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS WAS USED
REMARK 3 IN THE REFINEMENT PROTOCOL.
REMARK 4
REMARK 4 1GM1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-01.
REMARK 100 THE DEPOSITION ID IS D_1290008455.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.3
REMARK 210 IONIC STRENGTH : 100
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N NOESY-HSQC; 13C NOESYHSQC;
REMARK 210 13C NOESY-TROSY; HNHA; HCACO[N]
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XPLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED
REMARK 210 MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9
REMARK 210
REMARK 210 REMARK: THE ENSEMBLE WAS DETERMINED USING 3D TRIPLE RESONANCE NMR
REMARK 210 SPECTROSCOPY USING SINGLE AND DOUBLE-LABELED PDZ2.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 4 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 4 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 4 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 5 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 5 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 5 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 6 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 6 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 6 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 6 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 7 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 8 PHE A 14 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 8 PHE A 14 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 9 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 9 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 9 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 10 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 10 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 10 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 11 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 12 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 12 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 13 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 14 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 16 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 16 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 17 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 18 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 19 PHE A 14 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 19 PHE A 14 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 23 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 23 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 23 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 24 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 24 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 24 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 25 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 25 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 26 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 26 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 27 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 32 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 33 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 33 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ASP A 22 63.29 29.64
REMARK 500 1 THR A 35 -139.97 -94.76
REMARK 500 1 LYS A 50 21.33 82.47
REMARK 500 1 ASN A 87 43.16 -88.97
REMARK 500 1 GLN A 100 -62.01 -97.01
REMARK 500 2 ASN A 87 48.58 -88.51
REMARK 500 3 GLU A 17 78.06 -102.55
REMARK 500 3 LEU A 25 -61.59 -100.71
REMARK 500 3 ARG A 38 120.62 78.71
REMARK 500 3 HIS A 39 -69.77 72.47
REMARK 500 3 LYS A 50 26.53 81.74
REMARK 500 3 ASN A 87 48.81 -78.02
REMARK 500 4 ASN A 34 -64.29 -97.88
REMARK 500 4 ARG A 38 67.24 38.75
REMARK 500 4 HIS A 39 -3.21 69.27
REMARK 500 4 ASN A 87 43.06 -81.04
REMARK 500 5 PRO A 10 23.22 -76.20
REMARK 500 5 ASP A 22 52.12 33.34
REMARK 500 5 LEU A 25 -60.24 -101.28
REMARK 500 5 SER A 36 46.09 -83.28
REMARK 500 5 HIS A 39 19.21 56.69
REMARK 500 5 LYS A 50 20.35 82.29
REMARK 500 5 ASN A 87 39.71 -91.60
REMARK 500 6 SER A 36 36.38 -84.12
REMARK 500 6 ASN A 87 46.22 -86.52
REMARK 500 7 PRO A 10 63.84 -62.34
REMARK 500 7 THR A 35 -135.62 -87.57
REMARK 500 7 LYS A 50 16.34 83.01
REMARK 500 7 ASP A 56 -70.28 -58.91
REMARK 500 7 LEU A 73 32.62 -87.15
REMARK 500 7 ASN A 87 49.82 -94.83
REMARK 500 8 PRO A 10 -177.26 -69.82
REMARK 500 8 LEU A 25 -61.37 -106.65
REMARK 500 8 VAL A 37 -128.83 -100.34
REMARK 500 8 HIS A 39 65.43 151.34
REMARK 500 8 LYS A 50 20.16 82.50
REMARK 500 8 LEU A 73 39.32 -92.27
REMARK 500 8 ASN A 87 53.48 -94.39
REMARK 500 9 THR A 21 -149.81 -97.03
REMARK 500 9 HIS A 39 -68.99 -123.98
REMARK 500 9 LYS A 50 21.76 82.07
REMARK 500 9 LEU A 73 35.96 -99.45
REMARK 500 10 LEU A 25 -63.15 -102.84
REMARK 500 10 THR A 35 -155.94 -116.35
REMARK 500 10 ASN A 87 36.63 -95.65
REMARK 500 11 LEU A 25 -60.58 -99.96
REMARK 500 11 ARG A 38 98.02 82.44
REMARK 500 11 HIS A 39 -73.43 66.55
REMARK 500 11 LEU A 73 44.20 -85.48
REMARK 500 12 ARG A 38 104.74 -53.64
REMARK 500
REMARK 500 THIS ENTRY HAS 144 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ILE A 27 SER A 28 5 149.48
REMARK 500 GLY A 57 ARG A 58 8 146.57
REMARK 500 GLY A 57 ARG A 58 25 147.84
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 4 ARG A 86 0.12 SIDE CHAIN
REMARK 500 5 PHE A 14 0.09 SIDE CHAIN
REMARK 500 11 ARG A 58 0.11 SIDE CHAIN
REMARK 500 13 ARG A 64 0.11 SIDE CHAIN
REMARK 500 14 ARG A 38 0.09 SIDE CHAIN
REMARK 500 15 ARG A 38 0.09 SIDE CHAIN
REMARK 500 15 ARG A 58 0.09 SIDE CHAIN
REMARK 500 18 ARG A 58 0.11 SIDE CHAIN
REMARK 500 19 ARG A 38 0.08 SIDE CHAIN
REMARK 500 20 ARG A 38 0.08 SIDE CHAIN
REMARK 500 20 ARG A 86 0.08 SIDE CHAIN
REMARK 500 21 ARG A 58 0.13 SIDE CHAIN
REMARK 500 22 ARG A 86 0.08 SIDE CHAIN
REMARK 500 23 ARG A 38 0.08 SIDE CHAIN
REMARK 500 24 ARG A 58 0.11 SIDE CHAIN
REMARK 500 27 ARG A 38 0.08 SIDE CHAIN
REMARK 500 28 ARG A 58 0.08 SIDE CHAIN
REMARK 500 28 ARG A 64 0.09 SIDE CHAIN
REMARK 500 29 ARG A 64 0.12 SIDE CHAIN
REMARK 500 30 ARG A 58 0.10 SIDE CHAIN
REMARK 500 30 ARG A 64 0.09 SIDE CHAIN
REMARK 500 33 ARG A 58 0.11 SIDE CHAIN
REMARK 500 34 ARG A 38 0.07 SIDE CHAIN
REMARK 500 34 ARG A 58 0.11 SIDE CHAIN
REMARK 500 35 ARG A 58 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS ARE DEFINED.
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6092 RELATED DB: BMRB
DBREF 1GM1 A 9 102 UNP Q64512 Q64512 1351 1444
SEQRES 1 A 94 LYS PRO GLY ASP THR PHE GLU VAL GLU LEU ALA LYS THR
SEQRES 2 A 94 ASP GLY SER LEU GLY ILE SER VAL THR GLY GLY VAL ASN
SEQRES 3 A 94 THR SER VAL ARG HIS GLY GLY ILE TYR VAL LYS ALA ILE
SEQRES 4 A 94 ILE PRO LYS GLY ALA ALA GLU SER ASP GLY ARG ILE HIS
SEQRES 5 A 94 LYS GLY ASP ARG VAL LEU ALA VAL ASN GLY VAL SER LEU
SEQRES 6 A 94 GLU GLY ALA THR HIS LYS GLN ALA VAL GLU THR LEU ARG
SEQRES 7 A 94 ASN THR GLY GLN VAL VAL HIS LEU LEU LEU GLU LYS GLY
SEQRES 8 A 94 GLN VAL PRO
HELIX 1 1 ALA A 52 ASP A 56 1 5
HELIX 2 2 HIS A 78 ARG A 86 1 9
SHEET 1 AA 5 ASP A 12 ALA A 19 0
SHEET 2 AA 5 VAL A 91 LYS A 98 -1 O VAL A 92 N LEU A 18
SHEET 3 AA 5 ARG A 64 VAL A 68 -1 O ARG A 64 N GLU A 97
SHEET 4 AA 5 ILE A 42 ILE A 47 -1 O ILE A 42 N VAL A 65
SHEET 5 AA 5 ILE A 27 GLY A 31 -1 O SER A 28 N LYS A 45
SHEET 1 AB 4 ASP A 12 ALA A 19 0
SHEET 2 AB 4 VAL A 91 LYS A 98 -1 O VAL A 92 N LEU A 18
SHEET 3 AB 4 ARG A 64 VAL A 68 -1 O ARG A 64 N GLU A 97
SHEET 4 AB 4 VAL A 71 SER A 72 -1 O VAL A 71 N VAL A 68
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - r 28 2 Bytes