Header list of 1qdp.pdb file
Complete list - r 2 2 Bytes
HEADER NEUROTOXIN 09-OCT-97 1QDP
TITLE SOLUTION STRUCTURE OF ROBUSTOXIN, THE LETHAL NEUROTOXIN FROM THE
TITLE 2 FUNNEL WEB SPIDER ATRAX ROBUSTUS, NMR, 20 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ROBUSTOXIN;
COMPND 3 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ATRAX ROBUSTUS;
SOURCE 3 ORGANISM_TAXID: 6903;
SOURCE 4 ORGAN: VENOM GLAND
KEYWDS NEUROTOXIN, ATRAX ROBUSTUS, ROBUSTOXIN, CYSTINE KNOT, INHIBITOR
KEYWDS 2 CYSTINE KNOT MOTIF, SODIUM CHANNEL MODULATOR, FUNNEL WEB SPIDER,
KEYWDS 3 VENOM
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.K.PALLAGHY,D.ALEWOOD,P.F.ALEWOOD,R.S.NORTON
REVDAT 3 02-MAR-22 1QDP 1 REMARK
REVDAT 2 24-FEB-09 1QDP 1 VERSN
REVDAT 1 14-JAN-98 1QDP 0
JRNL AUTH P.K.PALLAGHY,D.ALEWOOD,P.F.ALEWOOD,R.S.NORTON
JRNL TITL SOLUTION STRUCTURE OF ROBUSTOXIN, THE LETHAL NEUROTOXIN FROM
JRNL TITL 2 THE FUNNEL-WEB SPIDER ATRAX ROBUSTUS.
JRNL REF FEBS LETT. V. 419 191 1997
JRNL REFN ISSN 0014-5793
JRNL PMID 9428632
JRNL DOI 10.1016/S0014-5793(97)01452-X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.0
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED SIMULATED ANNEALING OF DIANA
REMARK 3 STRUCTURES
REMARK 4
REMARK 4 1QDP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000175912.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 279
REMARK 210 PH : 5.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY; DQF; AMIDE
REMARK 210 EXCHANGE
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX-600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DYANA/X-PLOR
REMARK 210 METHOD USED : RESTRAINED SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL, NOE & DIHEDRAL ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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: 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 3 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES
REMARK 500 3 TYR A 22 CA - CB - CG ANGL. DEV. = -11.6 DEGREES
REMARK 500 3 TYR A 22 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 3 CYS A 31 CA - CB - SG ANGL. DEV. = 7.3 DEGREES
REMARK 500 3 CYS A 42 CA - CB - SG ANGL. DEV. = 7.4 DEGREES
REMARK 500 4 MET A 18 CG - SD - CE ANGL. DEV. = -11.9 DEGREES
REMARK 500 5 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES
REMARK 500 6 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 6 CYS A 31 CA - CB - SG ANGL. DEV. = 7.2 DEGREES
REMARK 500 7 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 8 CYS A 16 CA - CB - SG ANGL. DEV. = 7.9 DEGREES
REMARK 500 8 CYS A 42 CA - CB - SG ANGL. DEV. = 6.9 DEGREES
REMARK 500 9 TYR A 25 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 10 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 10 CYS A 16 CA - CB - SG ANGL. DEV. = 8.6 DEGREES
REMARK 500 10 MET A 18 CG - SD - CE ANGL. DEV. = -11.9 DEGREES
REMARK 500 10 CYS A 42 CA - CB - SG ANGL. DEV. = 6.8 DEGREES
REMARK 500 11 CYS A 16 CA - CB - SG ANGL. DEV. = 7.4 DEGREES
REMARK 500 11 TYR A 25 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 11 TYR A 25 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 11 CYS A 31 CA - CB - SG ANGL. DEV. = 6.8 DEGREES
REMARK 500 12 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 12 CYS A 31 CA - CB - SG ANGL. DEV. = 9.1 DEGREES
REMARK 500 12 CYS A 42 CA - CB - SG ANGL. DEV. = 9.6 DEGREES
REMARK 500 13 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 14 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 14 CYS A 31 CA - CB - SG ANGL. DEV. = 9.1 DEGREES
REMARK 500 15 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 16 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 16 CYS A 31 CA - CB - SG ANGL. DEV. = 7.2 DEGREES
REMARK 500 17 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES
REMARK 500 17 CYS A 14 CA - CB - SG ANGL. DEV. = 8.0 DEGREES
REMARK 500 18 ARG A 5 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES
REMARK 500 18 CYS A 16 CA - CB - SG ANGL. DEV. = 7.5 DEGREES
REMARK 500 18 CYS A 31 CA - CB - SG ANGL. DEV. = 6.9 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 ARG A 5 -46.90 137.04
REMARK 500 1 ASN A 11 47.62 -73.53
REMARK 500 1 ASP A 13 70.05 -115.40
REMARK 500 1 CYS A 16 156.11 -39.00
REMARK 500 1 ALA A 23 -100.13 -127.81
REMARK 500 1 TRP A 24 -54.64 -131.54
REMARK 500 1 ASN A 26 -176.63 65.50
REMARK 500 1 GLN A 27 -45.05 98.21
REMARK 500 1 ILE A 35 -56.71 76.00
REMARK 500 1 LEU A 38 -58.44 -158.51
REMARK 500 1 LYS A 40 64.50 -107.18
REMARK 500 2 LYS A 4 -178.81 65.08
REMARK 500 2 ARG A 5 -59.24 73.16
REMARK 500 2 ASN A 11 -33.59 -25.97
REMARK 500 2 GLU A 12 -60.52 -27.48
REMARK 500 2 CYS A 16 154.81 -38.56
REMARK 500 2 TYR A 22 -62.30 -130.19
REMARK 500 2 ALA A 23 -135.63 108.89
REMARK 500 2 TYR A 25 163.39 -44.78
REMARK 500 2 GLN A 28 -168.03 48.03
REMARK 500 2 ILE A 35 -52.39 75.32
REMARK 500 2 THR A 36 38.25 -147.54
REMARK 500 2 LEU A 38 -63.43 -141.36
REMARK 500 2 PHE A 39 54.56 -93.54
REMARK 500 2 LYS A 41 78.14 53.98
REMARK 500 3 LYS A 4 -179.75 67.05
REMARK 500 3 ARG A 5 -53.36 69.58
REMARK 500 3 ASN A 11 -35.68 -25.85
REMARK 500 3 GLU A 12 -75.17 -10.90
REMARK 500 3 CYS A 16 155.33 -38.42
REMARK 500 3 ILE A 21 168.60 -26.04
REMARK 500 3 GLN A 27 -62.65 136.39
REMARK 500 3 GLN A 28 -166.46 -123.41
REMARK 500 3 CYS A 31 98.63 -57.89
REMARK 500 3 ILE A 35 -50.52 77.65
REMARK 500 3 THR A 36 42.36 -150.03
REMARK 500 3 LEU A 38 -53.89 -153.14
REMARK 500 3 PHE A 39 59.85 -108.43
REMARK 500 3 LYS A 41 75.07 64.03
REMARK 500 4 LYS A 4 -175.63 63.78
REMARK 500 4 ARG A 5 -50.88 69.92
REMARK 500 4 CYS A 16 160.10 -38.95
REMARK 500 4 ALA A 23 -153.56 -130.82
REMARK 500 4 GLN A 27 -55.90 126.90
REMARK 500 4 ILE A 35 -57.48 82.36
REMARK 500 4 THR A 36 40.19 -146.10
REMARK 500 4 LEU A 38 -55.84 -150.88
REMARK 500 4 PHE A 39 44.84 -96.14
REMARK 500 4 LYS A 41 74.15 -118.45
REMARK 500 5 LYS A 4 152.72 -47.13
REMARK 500
REMARK 500 THIS ENTRY HAS 253 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 ARG A 5 0.31 SIDE CHAIN
REMARK 500 2 ARG A 5 0.32 SIDE CHAIN
REMARK 500 3 ARG A 5 0.31 SIDE CHAIN
REMARK 500 4 ARG A 5 0.31 SIDE CHAIN
REMARK 500 5 ARG A 5 0.31 SIDE CHAIN
REMARK 500 6 ARG A 5 0.32 SIDE CHAIN
REMARK 500 7 ARG A 5 0.28 SIDE CHAIN
REMARK 500 8 ARG A 5 0.29 SIDE CHAIN
REMARK 500 9 ARG A 5 0.29 SIDE CHAIN
REMARK 500 10 ARG A 5 0.31 SIDE CHAIN
REMARK 500 11 ARG A 5 0.31 SIDE CHAIN
REMARK 500 12 ARG A 5 0.32 SIDE CHAIN
REMARK 500 13 ARG A 5 0.31 SIDE CHAIN
REMARK 500 14 ARG A 5 0.31 SIDE CHAIN
REMARK 500 15 ARG A 5 0.31 SIDE CHAIN
REMARK 500 16 ARG A 5 0.32 SIDE CHAIN
REMARK 500 17 ARG A 5 0.30 SIDE CHAIN
REMARK 500 18 ARG A 5 0.31 SIDE CHAIN
REMARK 500 19 ARG A 5 0.32 SIDE CHAIN
REMARK 500 20 ARG A 5 0.30 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1QDP A 1 42 UNP P01478 TXDT1_ATRRO 1 42
SEQRES 1 A 42 CYS ALA LYS LYS ARG ASN TRP CYS GLY LYS ASN GLU ASP
SEQRES 2 A 42 CYS CYS CYS PRO MET LYS CYS ILE TYR ALA TRP TYR ASN
SEQRES 3 A 42 GLN GLN GLY SER CYS GLN THR THR ILE THR GLY LEU PHE
SEQRES 4 A 42 LYS LYS CYS
SHEET 1 A 2 LYS A 19 ILE A 21 0
SHEET 2 A 2 SER A 30 GLN A 32 -1 N GLN A 32 O LYS A 19
SSBOND 1 CYS A 1 CYS A 15 1555 1555 2.02
SSBOND 2 CYS A 8 CYS A 20 1555 1555 2.03
SSBOND 3 CYS A 14 CYS A 31 1555 1555 2.02
SSBOND 4 CYS A 16 CYS A 42 1555 1555 2.02
CISPEP 1 CYS A 16 PRO A 17 1 2.87
CISPEP 2 CYS A 16 PRO A 17 2 3.66
CISPEP 3 CYS A 16 PRO A 17 3 8.75
CISPEP 4 CYS A 16 PRO A 17 4 -0.76
CISPEP 5 CYS A 16 PRO A 17 5 12.58
CISPEP 6 CYS A 16 PRO A 17 6 16.24
CISPEP 7 CYS A 16 PRO A 17 7 -5.79
CISPEP 8 CYS A 16 PRO A 17 8 19.63
CISPEP 9 CYS A 16 PRO A 17 9 12.09
CISPEP 10 CYS A 16 PRO A 17 10 10.17
CISPEP 11 CYS A 16 PRO A 17 11 6.88
CISPEP 12 CYS A 16 PRO A 17 12 -10.77
CISPEP 13 CYS A 16 PRO A 17 13 5.28
CISPEP 14 CYS A 16 PRO A 17 14 8.05
CISPEP 15 CYS A 16 PRO A 17 15 2.89
CISPEP 16 CYS A 16 PRO A 17 16 -2.46
CISPEP 17 CYS A 16 PRO A 17 17 -2.48
CISPEP 18 CYS A 16 PRO A 17 18 4.95
CISPEP 19 CYS A 16 PRO A 17 19 7.39
CISPEP 20 CYS A 16 PRO A 17 20 8.01
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