Header list of 1s4g.pdb file
Complete list - r 2 2 Bytes
HEADER CELL ADHESION 16-JAN-04 1S4G TITLE SOMATOMEDIN-B DOMAIN OF HUMAN PLASMA VITRONECTIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITRONECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOMATOMEDIN B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: PLASMA KEYWDS SOMATOMEDIN B DOMAIN, DISULFIDE KNOT, VITRONECTIN, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.MAYASUNDARI,N.A.WHITTEMORE,E.H.SERPERSU,C.B.PETERSON REVDAT 4 02-MAR-22 1S4G 1 REMARK LINK REVDAT 3 24-FEB-09 1S4G 1 VERSN REVDAT 2 19-APR-05 1S4G 1 JRNL REVDAT 1 08-JUN-04 1S4G 0 JRNL AUTH A.MAYASUNDARI,N.A.WHITTEMORE,E.H.SERPERSU,C.B.PETERSON JRNL TITL THE SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN JRNL TITL 2 VITRONECTIN: PROXIMAL SITES THAT REGULATE FIBRINOLYSIS AND JRNL TITL 3 CELL MIGRATION JRNL REF J.BIOL.CHEM. V. 279 29359 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15123712 JRNL DOI 10.1074/JBC.M401279200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER DISCOVER 3 (2000), DISCOVER DISCOVER 3 REMARK 3 (2000) REMARK 3 AUTHORS : ACCELRYS (SAN DIEGO, CA) (DISCOVER), ACCELRYS (SAN REMARK 3 DIEGO, CA) (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 NOE CROSS-PEAK INTENSITIES WERE CONVERTED INTO DISTANCE RESTRAINTS REMARK 3 AS FOLLOWS: STRONG, 1.8-2.7 ; MEDIUM, 1.8-3.4 ; WEAK, 1.8-4.5 , REMARK 3 AND VERY WEAK 1.8-6.0. AN ADDITIONAL 1.0 WAS ADDED TO UPPER REMARK 3 LIMITS INVOLVING METHYL PROTONS, 0.5 FOR METHYLENE PROTONS AND 2.3 REMARK 3 FOR DEGENERATE HD AND HE PROTONS OF TYROSINES AND PHENYLALANINES. REMARK 3 ALSO, A 0.2 WAS ADDED TO THE UPPER LIMITS OF NOES INVOLVING AMIDE REMARK 3 PROTONS. BACKBONE F ANGLES WERE RESTRAINED TO -120 50 FOR 3JHNHA = REMARK 3 8-9 HZ, AND -120 40 FOR JHNHA > 9HZ. A RESTRAINT OF 100 80 REMARK 3 WAS ALSO APPLIED TO F ANGLE FOR RESIDUES THAT SHOW STRONGER NHI- REMARK 3 HAI-1 NOE THAN THE INTRARESIDUE NH-HA NOE. A TOTAL OF 329 NOE REMARK 3 RESTRAINTS AND 18 F RESTRAINTS WERE USED IN STRUCTURE REMARK 3 DETERMINATION. REMARK 3 RANDOM STRUCTURES WERE GENERATED BY SUBJECTING THE PEPTIDE TO AN REMARK 3 INITIAL 10000-STEP MINIMIZATION AT 298K. THE TEMPERATURE WAS THEN REMARK 3 RAISED GRADUALLY TO 1000K DURING A 1000 STEP DYNAMICS SIMULATION. REMARK 3 THE PEPTIDE WAS SUBJECTED TO MINIMIZATION AND A 10PS DYNAMICS AT REMARK 3 1000K. THE NMR-DERIVED RESTRAINTS WERE THEN IMPOSED ON THE REMARK 3 PEPTIDE AND THE PEPTIDE WAS SLOWLY ANNEALED TO 298K IN A 100PS REMARK 3 TRAJECTORY. FINALLY, THE STRUCTURES WERE SUBJECTED TO FURTHER REMARK 3 MINIMIZATION AT 298K. THE FORCE CONSTANT FOR THE DISTANCE REMARK 3 RESTRAINTS WAS 100 KCAL/MOL 2 AND THE DIELECTRIC CONSTANT WAS 4. REMARK 4 REMARK 4 1S4G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021354. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.4 REMARK 210 IONIC STRENGTH : LOW REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : ISOLATED FROM HUMAN PLASMA REMARK 210 VITRONECTIN BY CNBR CLEAVAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY 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 FELIX 2000, SPARKY, REMARK 210 MOLMOL, PROCHECK REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 VAL A 15 86.49 66.76 REMARK 500 1 CYS A 21 -63.61 -160.78 REMARK 500 1 ASP A 22 -102.12 -84.08 REMARK 500 1 GLU A 23 -68.96 75.77 REMARK 500 1 LEU A 24 -46.48 178.83 REMARK 500 1 GLN A 29 -108.59 75.01 REMARK 500 1 ASP A 34 -58.79 -139.92 REMARK 500 1 THR A 36 -79.83 -83.01 REMARK 500 1 GLN A 42 -63.27 -107.42 REMARK 500 1 ARG A 45 -68.32 67.44 REMARK 500 1 VAL A 48 -81.73 66.64 REMARK 500 2 SER A 4 73.82 55.56 REMARK 500 2 CYS A 5 89.21 61.72 REMARK 500 2 LYS A 6 -66.66 -131.75 REMARK 500 2 LYS A 17 -58.95 -137.14 REMARK 500 2 LYS A 18 -49.72 -152.99 REMARK 500 2 CYS A 19 93.37 151.70 REMARK 500 2 ASP A 34 -62.98 -131.87 REMARK 500 2 ARG A 45 -52.77 -153.55 REMARK 500 2 VAL A 48 -50.01 78.52 REMARK 500 2 THR A 50 -61.44 72.91 REMARK 500 3 SER A 4 133.76 74.04 REMARK 500 3 GLU A 11 -72.88 -79.71 REMARK 500 3 ASN A 14 -46.66 80.45 REMARK 500 3 VAL A 15 -169.57 -74.20 REMARK 500 3 CYS A 19 76.45 53.29 REMARK 500 3 CYS A 31 -57.89 68.85 REMARK 500 3 TYR A 35 -147.88 -126.42 REMARK 500 4 GLU A 3 -41.89 -160.26 REMARK 500 4 SER A 4 46.25 -155.03 REMARK 500 4 CYS A 5 60.80 34.98 REMARK 500 4 ARG A 8 45.53 -79.94 REMARK 500 4 ASP A 16 -91.63 33.61 REMARK 500 4 LYS A 17 55.73 -145.53 REMARK 500 4 CYS A 19 116.42 -162.25 REMARK 500 4 TYR A 27 -76.61 -94.07 REMARK 500 4 GLN A 29 -53.89 75.18 REMARK 500 4 SER A 30 68.68 77.65 REMARK 500 4 THR A 33 -55.90 72.99 REMARK 500 4 ASP A 34 -98.91 -77.23 REMARK 500 4 GLU A 38 166.81 67.85 REMARK 500 4 GLN A 42 -61.33 -143.25 REMARK 500 4 THR A 44 -66.89 -145.55 REMARK 500 4 VAL A 48 -61.62 73.05 REMARK 500 4 PHE A 49 103.81 -56.51 REMARK 500 5 GLN A 2 -84.42 53.15 REMARK 500 5 CYS A 19 156.58 74.84 REMARK 500 5 GLN A 20 -58.49 -137.87 REMARK 500 5 CYS A 21 77.59 -161.75 REMARK 500 5 GLU A 23 170.74 73.25 REMARK 500 REMARK 500 THIS ENTRY HAS 249 RAMACHANDRAN 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 TYR A 27 0.07 SIDE CHAIN REMARK 500 2 TYR A 27 0.12 SIDE CHAIN REMARK 500 4 TYR A 27 0.08 SIDE CHAIN REMARK 500 5 ARG A 8 0.09 SIDE CHAIN REMARK 500 5 TYR A 35 0.08 SIDE CHAIN REMARK 500 6 TYR A 28 0.07 SIDE CHAIN REMARK 500 7 TYR A 35 0.11 SIDE CHAIN REMARK 500 9 TYR A 27 0.10 SIDE CHAIN REMARK 500 9 TYR A 35 0.07 SIDE CHAIN REMARK 500 10 TYR A 35 0.06 SIDE CHAIN REMARK 500 13 TYR A 27 0.07 SIDE CHAIN REMARK 500 13 TYR A 28 0.07 SIDE CHAIN REMARK 500 13 TYR A 35 0.14 SIDE CHAIN REMARK 500 17 TYR A 28 0.09 SIDE CHAIN REMARK 500 17 TYR A 35 0.08 SIDE CHAIN REMARK 500 18 TYR A 27 0.08 SIDE CHAIN REMARK 500 19 TYR A 27 0.07 SIDE CHAIN REMARK 500 19 TYR A 35 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OH A 52 DBREF 1S4G A 1 51 UNP P04004 VTNC_HUMAN 20 70 SEQRES 1 A 51 ASP GLN GLU SER CYS LYS GLY ARG CYS THR GLU GLY PHE SEQRES 2 A 51 ASN VAL ASP LYS LYS CYS GLN CYS ASP GLU LEU CYS SER SEQRES 3 A 51 TYR TYR GLN SER CYS CYS THR ASP TYR THR ALA GLU CYS SEQRES 4 A 51 LYS PRO GLN VAL THR ARG GLY ASP VAL PHE THR MET HET OH A 52 2 HETNAM OH HYDROXIDE ION FORMUL 2 OH H O 1- SSBOND 1 CYS A 5 CYS A 9 1555 1555 2.05 SSBOND 2 CYS A 19 CYS A 31 1555 1555 2.04 SSBOND 3 CYS A 21 CYS A 32 1555 1555 2.06 SSBOND 4 CYS A 25 CYS A 39 1555 1555 2.05 LINK C MET A 51 O OH A 52 1555 1555 1.36 SITE 1 AC1 2 THR A 50 MET A 51 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