Header list of 1q5w.pdb file
Complete list - r 2 2 Bytes
HEADER PROTEIN BINDING 11-AUG-03 1Q5W
TITLE UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HOMOLOG OF YEAST NUCLEAR PROTEIN LOCALIZATION 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: NPL4 NZF DOMAIN (RESIDUES 580-608);
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: UBIQUITIN;
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: NORWAY RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: NPL4;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: T7;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX2T;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 GENE: (UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR
SOURCE 16 RPS27A);
SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: T7;
SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET3D
KEYWDS UBIQUITIN, PROTEIN-PROTEIN COMPLEX, ZINC-FINGER, RUBREDOXIN KNUCKLE,
KEYWDS 2 NZF DOMAIN, PROTEIN BINDING
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR S.L.ALAM,J.SUN,M.PAYNE,B.D.WELCH,B.K.BLAKE,D.R.DAVIS,H.H.MEYER,
AUTHOR 2 S.D.EMR,W.I.SUNDQUIST
REVDAT 4 02-MAR-22 1Q5W 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1Q5W 1 VERSN
REVDAT 2 13-APR-04 1Q5W 1 JRNL
REVDAT 1 30-MAR-04 1Q5W 0
JRNL AUTH S.L.ALAM,J.SUN,M.PAYNE,B.D.WELCH,B.K.BLAKE,D.R.DAVIS,
JRNL AUTH 2 H.H.MEYER,S.D.EMR,W.I.SUNDQUIST
JRNL TITL UBIQUITIN INTERACTIONS OF NZF ZINC FINGERS.
JRNL REF EMBO J. V. 23 1411 2004
JRNL REFN ISSN 0261-4189
JRNL PMID 15029239
JRNL DOI 10.1038/SJ.EMBOJ.7600114
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH B.WANG,S.L.ALAM,H.H.MEYER,M.PAYNE,T.L.STEMMLER,D.R.DAVIS,
REMARK 1 AUTH 2 W.I.SUNDQUIST
REMARK 1 TITL STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED ZINC
REMARK 1 TITL 2 FINGER DOMAIN OF NPL4.
REMARK 1 REF J.BIOL.CHEM. V. 278 20225 2003
REMARK 1 REFN ISSN 0021-9258
REMARK 1 DOI 10.1074/JBC.M300459200
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.5, CNS 1.1
REMARK 3 AUTHORS : PETER GUNTERT (DYANA), "CRYSTALLOGRAPHY AND NMR
REMARK 3 SYSTEM (CNS): A NEW SOFTWARE SYSTEM (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 STRUCTURES ARE BASED ON 2072 NOE-DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 145 DIHEDRAL ANGLE CONSTRAINTS ,104 H-BOND
REMARK 3 CONSTRAINTS, AND 14 ZINC-COORDINATION CONSTRAINTS.
REMARK 4
REMARK 4 1Q5W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-03.
REMARK 100 THE DEPOSITION ID IS D_1000019955.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 291; 291; 291; 291
REMARK 210 PH : 5.5; 5.5; 5.5; 5.5
REMARK 210 IONIC STRENGTH : 70MM; 70MM; 70MM; 70MM
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT;
REMARK 210 AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM NPL4 NZF U-15N,13C; 2MM
REMARK 210 UNLABELED-UBIQUITIN; 20MM
REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM
REMARK 210 NACL; 90% H2O, 10%; 1MM
REMARK 210 UBIQUITIN U-15N,13C; 2MM
REMARK 210 UNLABELED-NPL4 NZF; 20MM
REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM
REMARK 210 NACL; 90% H2O, 10%; 1MM
REMARK 210 UBIQUITIN U-15N; 2MM UNLABELED-
REMARK 210 NPL4 NZF; 20MM PHOSPHATE BUFFER
REMARK 210 PH 5.5, 50MM; 1MM NPL4 NZF U-15N;
REMARK 210 2MM UNLABELED-UBIQUITIN; 20MM
REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM
REMARK 210 NACL; 90% H2O, 10%
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; HNCACB,
REMARK 210 CBCACONH, CCONH, HCCONH,HNCO,
REMARK 210 HNCACO
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 97, SPARKY 3.106
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS FOLLOWED
REMARK 210 BY SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY,TARGET
REMARK 210 FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: INTER-MOLECULAR NOES IDENTIFIED WITH HALF-FILTERED AND
REMARK 210 DOUBLE HALF-FILTERED NOE EXPERIMENTS AND SAMPLES #1 AND #2.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 SER A 4 -170.19 -65.56
REMARK 500 1 CYS A 9 157.59 -46.57
REMARK 500 1 HIS A 11 -57.86 -131.99
REMARK 500 1 THR A 13 23.53 81.06
REMARK 500 1 ASP B 121 -167.62 -63.98
REMARK 500 1 ASN B 160 44.04 86.63
REMARK 500 2 SER A 2 144.16 -176.64
REMARK 500 2 THR A 3 31.60 -98.90
REMARK 500 2 ALA A 5 122.90 -177.63
REMARK 500 2 CYS A 9 157.21 -47.57
REMARK 500 2 HIS A 11 -57.81 -132.31
REMARK 500 2 ASP B 121 -165.12 -61.92
REMARK 500 2 ASN B 160 51.46 85.74
REMARK 500 2 SER B 165 173.30 -59.00
REMARK 500 2 ARG B 174 -169.16 46.24
REMARK 500 3 THR A 3 102.41 -176.71
REMARK 500 3 ALA A 5 -176.23 62.07
REMARK 500 3 CYS A 9 157.45 -46.79
REMARK 500 3 HIS A 11 -54.11 -137.81
REMARK 500 3 THR A 13 74.19 54.77
REMARK 500 3 ASP B 121 -168.07 -65.29
REMARK 500 3 ALA B 146 41.69 39.13
REMARK 500 3 ASN B 160 50.47 83.89
REMARK 500 4 SER A 2 -40.43 -176.42
REMARK 500 4 ALA A 5 50.85 -92.62
REMARK 500 4 CYS A 9 157.41 -48.64
REMARK 500 4 HIS A 11 -57.37 -130.73
REMARK 500 4 MET A 25 -58.92 -123.02
REMARK 500 4 ASP B 121 -167.66 -64.37
REMARK 500 4 ASN B 160 49.72 84.29
REMARK 500 5 SER A 2 102.56 60.83
REMARK 500 5 SER A 4 -74.81 -127.99
REMARK 500 5 ALA A 5 50.30 -166.36
REMARK 500 5 CYS A 9 157.45 -47.78
REMARK 500 5 HIS A 11 -55.89 -135.25
REMARK 500 5 MET A 25 -59.65 -123.04
REMARK 500 5 ASP B 121 -165.60 -58.09
REMARK 500 5 ASN B 160 50.62 86.59
REMARK 500 5 SER B 165 171.96 -58.58
REMARK 500 6 SER A 2 106.58 -161.90
REMARK 500 6 THR A 3 155.62 60.36
REMARK 500 6 CYS A 9 157.19 -47.22
REMARK 500 6 HIS A 11 -56.80 -137.53
REMARK 500 6 ASP B 121 -165.28 -60.31
REMARK 500 6 ASN B 160 50.17 86.77
REMARK 500 7 SER A 2 113.79 61.62
REMARK 500 7 THR A 3 -69.36 -163.75
REMARK 500 7 ALA A 5 124.54 -176.82
REMARK 500 7 CYS A 9 157.41 -46.40
REMARK 500 7 HIS A 11 -54.36 -130.21
REMARK 500
REMARK 500 THIS ENTRY HAS 154 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 32 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 9 SG
REMARK 620 2 CYS A 12 SG 107.4
REMARK 620 3 CYS A 23 SG 104.2 113.0
REMARK 620 4 CYS A 26 SG 103.7 124.8 101.7
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 32
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1NJ3 RELATED DB: PDB
REMARK 900 NPL4 ZINC FINGER STRUCTURE
DBREF 1Q5W A 3 31 UNP Q9ES54 NPL4_RAT 580 608
DBREF 1Q5W B 101 176 UNP P62988 UBIQ_HUMAN 1 76
SEQADV 1Q5W GLY A 1 UNP Q9ES54 CLONING ARTIFACT
SEQADV 1Q5W SER A 2 UNP Q9ES54 CLONING ARTIFACT
SEQRES 1 A 31 GLY SER THR SER ALA MET TRP ALA CYS GLN HIS CYS THR
SEQRES 2 A 31 PHE MET ASN GLN PRO GLY THR GLY HIS CYS GLU MET CYS
SEQRES 3 A 31 SER LEU PRO ARG THR
SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
HET ZN A 32 1
HETNAM ZN ZINC ION
FORMUL 3 ZN ZN 2+
HELIX 1 1 THR B 122 GLU B 134 1 13
SHEET 1 A 2 TRP A 7 ALA A 8 0
SHEET 2 A 2 MET A 15 ASN A 16 -1 O ASN A 16 N TRP A 7
SHEET 1 B 4 THR B 112 GLU B 116 0
SHEET 2 B 4 GLN B 102 THR B 107 -1 N VAL B 105 O ILE B 113
SHEET 3 B 4 SER B 165 LEU B 171 1 O LEU B 167 N PHE B 104
SHEET 4 B 4 GLN B 141 ILE B 144 -1 N ILE B 144 O HIS B 168
LINK SG CYS A 9 ZN ZN A 32 1555 1555 2.38
LINK SG CYS A 12 ZN ZN A 32 1555 1555 2.32
LINK SG CYS A 23 ZN ZN A 32 1555 1555 2.41
LINK SG CYS A 26 ZN ZN A 32 1555 1555 2.38
SITE 1 AC1 4 CYS A 9 CYS A 12 CYS A 23 CYS A 26
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 2 2 Bytes