Header list of 1dqb.pdb file
Complete list - l 29 2 Bytes
HEADER MEMBRANE PROTEIN 03-JAN-00 1DQB
TITLE NMR STRUCTURE OF THROMBOMODULIN EGF(4-5)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBOMODULIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: THE FOURTH AND FIFTH EGF-LIKE DOMAINS;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: RESIDUES 346-426
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 CELL: ENDOTHELIAL;
SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: SMD1168
KEYWDS THROMBIN, EGF MODULE, ANTICOAGULANT, GLYCOSYLATION, MEMBRANE PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 12
AUTHOR M.J.WOOD,B.A.SAMPOLI-BENITEZ,E.A.KOMIVES
REVDAT 5 29-JUL-20 1DQB 1 COMPND REMARK SEQADV HETNAM
REVDAT 5 2 1 LINK SITE
REVDAT 4 13-JUL-11 1DQB 1 VERSN
REVDAT 3 24-FEB-09 1DQB 1 VERSN
REVDAT 2 23-SEP-03 1DQB 1 JRNL DBREF
REVDAT 1 06-MAR-00 1DQB 0
JRNL AUTH M.J.WOOD,B.A.SAMPOLI-BENITEZ,E.A.KOMIVES
JRNL TITL SOLUTION STRUCTURE OF THE SMALLEST COFACTOR-ACTIVE FRAGMENT
JRNL TITL 2 OF THROMBOMODULIN.
JRNL REF NAT.STRUCT.BIOL. V. 7 200 2000
JRNL REFN ISSN 1072-8368
JRNL PMID 10700277
JRNL DOI 10.1038/73302
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.0, X-PLOR 3.5
REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 985 NOE
REMARK 3 DISTANCE RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS AND 16
REMARK 3 STREOSPECIFIC ASSIGNMENTS.
REMARK 4
REMARK 4 1DQB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-00.
REMARK 100 THE DEPOSITION ID IS D_1000010288.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 310
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 0
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1MM TM45 U-15N; 90% H2O, 10%
REMARK 210 D2O, PH 6.5; 1MM TM45; 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNHA; 2D
REMARK 210 NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 97.0, DGII 97.0
REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED
REMARK 210 ANNEALING REFINMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS CALCULATED USING NOES FROM THE 3D NOESY
REMARK 210 -HSQC AND D2O NOESY AND DIHEDRAL ANGLES FROM THE HNHA.
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
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 MET A 2 -166.57 73.45
REMARK 500 1 GLU A 3 126.37 -177.74
REMARK 500 1 VAL A 5 114.30 -3.47
REMARK 500 1 ASP A 6 -92.90 -40.66
REMARK 500 1 CYS A 8 -99.18 -92.61
REMARK 500 1 PHE A 9 46.96 21.65
REMARK 500 1 ARG A 10 -11.77 175.92
REMARK 500 1 ALA A 11 -81.12 -53.05
REMARK 500 1 ASN A 12 54.17 -158.13
REMARK 500 1 CYS A 13 109.48 -21.90
REMARK 500 1 GLU A 14 -77.03 -47.96
REMARK 500 1 TYR A 15 -131.15 -57.81
REMARK 500 1 GLN A 16 -158.22 -130.08
REMARK 500 1 LEU A 20 -77.36 119.38
REMARK 500 1 GLN A 22 40.53 31.82
REMARK 500 1 SER A 24 137.43 41.25
REMARK 500 1 LEU A 26 -130.73 -115.61
REMARK 500 1 CYS A 29 -156.13 -135.19
REMARK 500 1 GLU A 31 11.58 -69.64
REMARK 500 1 ALA A 34 158.44 179.63
REMARK 500 1 PRO A 35 85.40 -51.15
REMARK 500 1 ILE A 36 163.23 -29.95
REMARK 500 1 PRO A 37 52.78 -36.30
REMARK 500 1 HIS A 38 -102.61 168.91
REMARK 500 1 PRO A 40 61.34 -60.89
REMARK 500 1 GLN A 44 79.41 175.69
REMARK 500 1 MET A 45 -170.62 -38.16
REMARK 500 1 ALA A 51 123.66 38.22
REMARK 500 1 ALA A 54 -150.48 -12.53
REMARK 500 1 CYS A 56 -157.07 -32.13
REMARK 500 1 PRO A 58 -88.02 -66.12
REMARK 500 1 GLN A 61 75.71 -32.59
REMARK 500 1 ALA A 62 26.16 -64.69
REMARK 500 1 SER A 63 84.20 -164.09
REMARK 500 1 GLU A 65 -77.40 -50.95
REMARK 500 1 CYS A 66 40.22 -81.85
REMARK 500 1 GLU A 68 79.17 -20.69
REMARK 500 1 TYR A 70 138.76 22.57
REMARK 500 1 LEU A 72 132.94 -3.80
REMARK 500 1 ASP A 73 35.04 150.01
REMARK 500 1 ASP A 74 -136.44 -29.23
REMARK 500 1 PHE A 76 38.19 175.28
REMARK 500 1 ILE A 77 -162.00 -78.58
REMARK 500 1 CYS A 78 52.14 101.99
REMARK 500 1 THR A 79 66.75 173.84
REMARK 500 1 ASP A 80 76.99 26.99
REMARK 500 1 ILE A 81 11.08 -62.38
REMARK 500 1 ASP A 82 -73.80 -57.42
REMARK 500 2 GLU A 3 146.89 9.63
REMARK 500 2 PRO A 4 32.33 -72.06
REMARK 500
REMARK 500 THIS ENTRY HAS 589 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 HIS A 1 MET A 2 1 140.23
REMARK 500 GLU A 3 PRO A 4 1 149.90
REMARK 500 PRO A 4 VAL A 5 1 -141.59
REMARK 500 VAL A 5 ASP A 6 1 -131.78
REMARK 500 ASP A 6 PRO A 7 1 80.32
REMARK 500 ARG A 10 ALA A 11 1 -123.65
REMARK 500 ALA A 11 ASN A 12 1 102.50
REMARK 500 ASN A 12 CYS A 13 1 143.94
REMARK 500 GLU A 14 TYR A 15 1 143.09
REMARK 500 GLN A 18 PRO A 19 1 -50.36
REMARK 500 PRO A 19 LEU A 20 1 144.83
REMARK 500 LEU A 20 ASN A 21 1 -126.00
REMARK 500 GLN A 22 THR A 23 1 99.64
REMARK 500 THR A 23 SER A 24 1 -129.99
REMARK 500 SER A 24 TYR A 25 1 -112.62
REMARK 500 TYR A 25 LEU A 26 1 -145.55
REMARK 500 LEU A 26 CYS A 27 1 118.04
REMARK 500 VAL A 28 CYS A 29 1 135.92
REMARK 500 ALA A 30 GLU A 31 1 -118.10
REMARK 500 ALA A 34 PRO A 35 1 -144.27
REMARK 500 ILE A 36 PRO A 37 1 145.84
REMARK 500 PRO A 37 HIS A 38 1 122.16
REMARK 500 HIS A 38 GLU A 39 1 -149.13
REMARK 500 PRO A 40 HIS A 41 1 133.31
REMARK 500 HIS A 41 ARG A 42 1 -138.65
REMARK 500 ARG A 42 CYS A 43 1 145.80
REMARK 500 CYS A 43 GLN A 44 1 149.51
REMARK 500 GLN A 44 MET A 45 1 -74.92
REMARK 500 MET A 45 PHE A 46 1 139.76
REMARK 500 PHE A 46 CYS A 47 1 149.86
REMARK 500 GLN A 49 THR A 50 1 84.18
REMARK 500 THR A 50 ALA A 51 1 -135.32
REMARK 500 ALA A 51 CYS A 52 1 95.70
REMARK 500 CYS A 52 PRO A 53 1 136.63
REMARK 500 PRO A 53 ALA A 54 1 122.31
REMARK 500 ASP A 55 CYS A 56 1 148.10
REMARK 500 ASP A 57 PRO A 58 1 127.05
REMARK 500 PRO A 58 ASN A 59 1 -128.07
REMARK 500 THR A 60 GLN A 61 1 -128.74
REMARK 500 ALA A 62 SER A 63 1 -127.61
REMARK 500 SER A 63 CYS A 64 1 86.44
REMARK 500 GLU A 65 CYS A 66 1 -141.47
REMARK 500 CYS A 66 PRO A 67 1 98.68
REMARK 500 PRO A 67 GLU A 68 1 -110.58
REMARK 500 GLU A 68 GLY A 69 1 74.54
REMARK 500 GLY A 69 TYR A 70 1 -136.52
REMARK 500 TYR A 70 ILE A 71 1 82.44
REMARK 500 ILE A 71 LEU A 72 1 139.74
REMARK 500 LEU A 72 ASP A 73 1 94.18
REMARK 500 ASP A 73 ASP A 74 1 138.32
REMARK 500
REMARK 500 THIS ENTRY HAS 585 NON CIS, NON-TRANS OMEGA OUTLIERS.
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 1 ARG A 10 0.26 SIDE CHAIN
REMARK 500 1 ARG A 42 0.32 SIDE CHAIN
REMARK 500 2 ARG A 10 0.24 SIDE CHAIN
REMARK 500 2 ARG A 42 0.32 SIDE CHAIN
REMARK 500 3 ARG A 10 0.32 SIDE CHAIN
REMARK 500 3 ARG A 42 0.29 SIDE CHAIN
REMARK 500 4 ARG A 10 0.27 SIDE CHAIN
REMARK 500 4 ARG A 42 0.12 SIDE CHAIN
REMARK 500 5 ARG A 10 0.31 SIDE CHAIN
REMARK 500 6 ARG A 42 0.22 SIDE CHAIN
REMARK 500 7 ARG A 10 0.11 SIDE CHAIN
REMARK 500 7 ARG A 42 0.10 SIDE CHAIN
REMARK 500 8 ARG A 10 0.23 SIDE CHAIN
REMARK 500 8 ARG A 42 0.28 SIDE CHAIN
REMARK 500 9 ARG A 10 0.31 SIDE CHAIN
REMARK 500 9 ARG A 42 0.24 SIDE CHAIN
REMARK 500 10 ARG A 10 0.25 SIDE CHAIN
REMARK 500 10 ARG A 42 0.23 SIDE CHAIN
REMARK 500 11 ARG A 10 0.22 SIDE CHAIN
REMARK 500 11 ARG A 42 0.11 SIDE CHAIN
REMARK 500 12 ARG A 10 0.24 SIDE CHAIN
REMARK 500 12 ARG A 42 0.27 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1ZAQ RELATED DB: PDB
REMARK 900 FOURTH EGF-LIKE DOMAIN OF THROMBOMODULIN. 12 NMR STRUCTURES.
REMARK 900 RELATED ID: 1ADX RELATED DB: PDB
REMARK 900 FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN. 14 NMR STRUCTURES.
REMARK 900 RELATED ID: 2ADX RELATED DB: PDB
REMARK 900 FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN. MINIMIZED AVERAGE
REMARK 900 STRUCTURE.
DBREF 1DQB A 1 83 UNP P07204 TRBM_HUMAN 344 426
SEQADV 1DQB HIS A 1 UNP P07204 CYS 344 CONFLICT
SEQADV 1DQB MET A 2 UNP P07204 VAL 345 CONFLICT
SEQRES 1 A 83 HIS MET GLU PRO VAL ASP PRO CYS PHE ARG ALA ASN CYS
SEQRES 2 A 83 GLU TYR GLN CYS GLN PRO LEU ASN GLN THR SER TYR LEU
SEQRES 3 A 83 CYS VAL CYS ALA GLU GLY PHE ALA PRO ILE PRO HIS GLU
SEQRES 4 A 83 PRO HIS ARG CYS GLN MET PHE CYS ASN GLN THR ALA CYS
SEQRES 5 A 83 PRO ALA ASP CYS ASP PRO ASN THR GLN ALA SER CYS GLU
SEQRES 6 A 83 CYS PRO GLU GLY TYR ILE LEU ASP ASP GLY PHE ILE CYS
SEQRES 7 A 83 THR ASP ILE ASP GLU
MODRES 1DQB ASN A 21 ASN GLYCOSYLATION SITE
MODRES 1DQB ASN A 48 ASN GLYCOSYLATION SITE
HET NAG A 121 28
HET NAG A 148 28
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
FORMUL 2 NAG 2(C8 H15 N O6)
SSBOND 1 CYS A 8 CYS A 17 1555 1555 2.03
SSBOND 2 CYS A 13 CYS A 27 1555 1555 2.04
SSBOND 3 CYS A 29 CYS A 43 1555 1555 2.04
SSBOND 4 CYS A 47 CYS A 52 1555 1555 2.04
SSBOND 5 CYS A 56 CYS A 64 1555 1555 2.04
SSBOND 6 CYS A 66 CYS A 78 1555 1555 2.04
LINK ND2 ASN A 21 C1 NAG A 121 1555 1555 1.45
LINK ND2 ASN A 48 C1 NAG A 148 1555 1555 1.45
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 - l 29 2 Bytes