Header list of 1znm.pdb file
Complete list - v 29 2 Bytes
HEADER ZINC FINGER 20-NOV-97 1ZNM
TITLE A ZINC FINGER WITH AN ARTIFICIAL BETA-TURN, ORIGINAL SEQUENCE TAKEN
TITLE 2 FROM THE THIRD ZINC FINGER DOMAIN OF THE HUMAN TRANSCRIPTIONAL
TITLE 3 REPRESSOR PROTEIN YY1 (YING AND YANG 1, A DELTA TRANSCRIPTION
TITLE 4 FACTOR), NMR, 34 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: YY1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ZINC FINGER DNA BINDING DOMAIN 3 FROM YY1;
COMPND 5 SYNONYM: ZN-BTD(7,8)-3YY1;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: DOES NOT BIND DNA SPECIFICALLY AS A SINGLE ZINC FINGER
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SEQUENCE SYNTHESISED USING FMOC CHEMISTRY, WITH BETA-
SOURCE 4 TURN MIMETIC BTD IN POSITIONS 7 AND 8
KEYWDS ZINC FINGER, ZN-BTD(7, 8)-3YY1, BETA-TURN MIMETIC, TRANSCRIPTION
KEYWDS 2 REGULATION
EXPDTA SOLUTION NMR
NUMMDL 34
AUTHOR J.H.VILES,S.U.PATEL,J.B.O.MITCHELL,C.M.MOODY,D.E.JUSTICE,
AUTHOR 2 J.UPPENBRINK,P.M.DOYLE,C.J.HARRIS,P.J.SADLER,J.M.THORNTON
REVDAT 3 29-NOV-17 1ZNM 1 REMARK HELIX
REVDAT 2 24-FEB-09 1ZNM 1 VERSN
REVDAT 1 01-APR-98 1ZNM 0
JRNL AUTH J.H.VILES,S.U.PATEL,J.B.MITCHELL,C.M.MOODY,D.E.JUSTICE,
JRNL AUTH 2 J.UPPENBRINK,P.M.DOYLE,C.J.HARRIS,P.J.SADLER,J.M.THORNTON
JRNL TITL DESIGN, SYNTHESIS AND STRUCTURE OF A ZINC FINGER WITH AN
JRNL TITL 2 ARTIFICIAL BETA-TURN.
JRNL REF J.MOL.BIOL. V. 279 973 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9642075
JRNL DOI 10.1006/JMBI.1998.1764
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED USING AN
REMARK 3 AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED
REMARK 3 WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI
REMARK 3 AND PSI ANGLES. THE ZINC ION WAS INCORPORATED WITH THE
REMARK 3 APPROPRIATE GEOMETRIC CONSTRAINTS TO PRODUCE TETRAHEDRAL ZINC CO-
REMARK 3 ORDINATION.
REMARK 4
REMARK 4 1ZNM 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_1000177497.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : ROESY; NOESY; COSY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; VXR600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 34
REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE VIOLATIONS ABOVE 0.2
REMARK 210 ANGSTROM AND 5 DEGREE DIHEDRAL
REMARK 210 ANGLE
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-34
REMARK 465 RES C SSSEQI
REMARK 465 PRO A 1
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 THR A 5 39.42 -164.12
REMARK 500 1 NVA A 7 -150.10 44.36
REMARK 500 1 HIS A 22 -72.23 -104.85
REMARK 500 2 THR A 5 36.96 -154.88
REMARK 500 2 NVA A 7 -157.48 50.30
REMARK 500 2 HIS A 22 -68.93 -101.90
REMARK 500 3 THR A 5 36.07 -162.00
REMARK 500 3 NVA A 7 -161.20 48.82
REMARK 500 3 SER A 14 -64.12 -94.44
REMARK 500 3 HIS A 22 -69.37 -104.19
REMARK 500 4 THR A 5 38.77 -140.67
REMARK 500 4 NVA A 7 -157.07 45.23
REMARK 500 4 HIS A 22 -69.31 -105.25
REMARK 500 5 THR A 5 39.23 -163.26
REMARK 500 5 NVA A 7 -150.38 46.31
REMARK 500 5 HIS A 22 -70.45 -100.66
REMARK 500 6 THR A 5 36.02 -162.88
REMARK 500 6 NVA A 7 -159.06 52.44
REMARK 500 6 HIS A 22 -70.23 -102.74
REMARK 500 7 THR A 5 36.11 -158.99
REMARK 500 7 NVA A 7 -157.35 51.96
REMARK 500 7 HIS A 22 -69.54 -102.53
REMARK 500 8 GLN A 3 105.32 -178.76
REMARK 500 8 THR A 5 42.04 -165.90
REMARK 500 8 NVA A 7 -152.25 51.50
REMARK 500 8 CYS A 9 -73.67 -79.26
REMARK 500 8 HIS A 22 -64.21 -92.21
REMARK 500 9 THR A 5 36.26 -158.25
REMARK 500 9 NVA A 7 -157.62 48.01
REMARK 500 9 HIS A 22 -71.74 -107.73
REMARK 500 9 LYS A 24 -19.90 -47.62
REMARK 500 10 GLN A 3 108.60 -179.06
REMARK 500 10 THR A 5 34.05 -172.91
REMARK 500 10 NVA A 7 -162.64 45.22
REMARK 500 10 SER A 14 -76.93 -75.74
REMARK 500 10 HIS A 22 -68.35 -106.64
REMARK 500 11 GLN A 3 148.63 -178.07
REMARK 500 11 THR A 5 38.13 -147.73
REMARK 500 11 NVA A 7 -157.75 43.08
REMARK 500 11 HIS A 22 -69.66 -104.15
REMARK 500 12 THR A 5 37.39 -149.80
REMARK 500 12 NVA A 7 -158.35 46.10
REMARK 500 12 SER A 14 -67.87 -94.39
REMARK 500 12 HIS A 22 -71.47 -89.85
REMARK 500 13 THR A 5 36.24 -156.82
REMARK 500 13 NVA A 7 -156.87 52.09
REMARK 500 13 SER A 14 -56.13 -120.55
REMARK 500 13 HIS A 22 -71.64 -92.11
REMARK 500 14 THR A 5 38.30 -145.22
REMARK 500 14 NVA A 7 -156.90 48.72
REMARK 500
REMARK 500 THIS ENTRY HAS 126 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 12 0.22 SIDE CHAIN
REMARK 500 2 ARG A 12 0.26 SIDE CHAIN
REMARK 500 3 ARG A 12 0.09 SIDE CHAIN
REMARK 500 4 ARG A 12 0.10 SIDE CHAIN
REMARK 500 5 ARG A 12 0.31 SIDE CHAIN
REMARK 500 6 ARG A 12 0.08 SIDE CHAIN
REMARK 500 7 ARG A 12 0.27 SIDE CHAIN
REMARK 500 8 ARG A 12 0.32 SIDE CHAIN
REMARK 500 9 ARG A 12 0.22 SIDE CHAIN
REMARK 500 10 ARG A 12 0.14 SIDE CHAIN
REMARK 500 11 ARG A 12 0.30 SIDE CHAIN
REMARK 500 12 ARG A 12 0.28 SIDE CHAIN
REMARK 500 13 ARG A 12 0.24 SIDE CHAIN
REMARK 500 14 ARG A 12 0.09 SIDE CHAIN
REMARK 500 15 ARG A 12 0.31 SIDE CHAIN
REMARK 500 16 ARG A 12 0.13 SIDE CHAIN
REMARK 500 17 ARG A 12 0.32 SIDE CHAIN
REMARK 500 18 ARG A 12 0.31 SIDE CHAIN
REMARK 500 19 ARG A 12 0.26 SIDE CHAIN
REMARK 500 20 ARG A 12 0.19 SIDE CHAIN
REMARK 500 21 ARG A 12 0.20 SIDE CHAIN
REMARK 500 22 ARG A 12 0.31 SIDE CHAIN
REMARK 500 23 ARG A 12 0.23 SIDE CHAIN
REMARK 500 24 ARG A 12 0.29 SIDE CHAIN
REMARK 500 25 ARG A 12 0.24 SIDE CHAIN
REMARK 500 26 ARG A 12 0.19 SIDE CHAIN
REMARK 500 27 ARG A 12 0.15 SIDE CHAIN
REMARK 500 28 ARG A 12 0.32 SIDE CHAIN
REMARK 500 29 ARG A 12 0.30 SIDE CHAIN
REMARK 500 30 ARG A 12 0.09 SIDE CHAIN
REMARK 500 31 ARG A 12 0.17 SIDE CHAIN
REMARK 500 32 ARG A 12 0.25 SIDE CHAIN
REMARK 500 33 ARG A 12 0.24 SIDE CHAIN
REMARK 500 34 ARG A 12 0.28 SIDE CHAIN
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 29 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 4 SG
REMARK 620 2 CYS A 9 SG 112.0
REMARK 620 3 HIS A 22 NE2 116.1 106.2
REMARK 620 4 HIS A 26 NE2 109.0 109.5 103.6
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ZNB
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: ZN BINDING SITE.
REMARK 800
REMARK 800 SITE_IDENTIFIER: BTD
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: BETA TURN DIPEPTIDE (TYPE II' BETA TURN
REMARK 800 MIMETIC).
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 29
DBREF 1ZNM A 1 28 UNP P25490 TYY1_HUMAN 352 379
SEQADV 1ZNM NVA A 7 UNP P25490 GLU 358 MODIFIED RESIDUE
SEQADV 1ZNM CYS A 8 UNP P25490 GLY 359 MODIFIED RESIDUE
SEQADV 1ZNM LYS A 20 UNP P25490 ARG 371 CONFLICT
SEQADV 1ZNM LYS A 24 UNP P25490 ARG 375 CONFLICT
SEQRES 1 A 28 PRO PHE GLN CYS THR PHE NVA CYS CYS GLY LYS ARG PHE
SEQRES 2 A 28 SER LEU ASP PHE ASN LEU LYS THR HIS VAL LYS ILE HIS
SEQRES 3 A 28 THR GLY
MODRES 1ZNM NVA A 7 VAL NORVALINE
HET NVA A 7 14
HET ZN A 29 1
HETNAM NVA NORVALINE
HETNAM ZN ZINC ION
FORMUL 1 NVA C5 H11 N O2
FORMUL 2 ZN ZN 2+
HELIX 1 1 ASP A 16 THR A 27 1SEE REMARK 650 12
SHEET 1 A 2 PHE A 2 PHE A 6 0
SHEET 2 A 2 LYS A 11 PHE A 13 -1 O PHE A 13 N PHE A 2
LINK N NVA A 7 C PHE A 6 1555 1555 1.30
LINK CD NVA A 7 N CYS A 8 1555 1555 1.51
LINK CD NVA A 7 SG CYS A 8 1555 1555 1.81
LINK C NVA A 7 N CYS A 8 1555 1555 1.31
LINK C CYS A 8 N CYS A 9 1555 1555 1.31
LINK ZN ZN A 29 SG CYS A 4 1555 1555 2.30
LINK ZN ZN A 29 SG CYS A 9 1555 1555 2.31
LINK ZN ZN A 29 NE2 HIS A 22 1555 1555 1.99
LINK ZN ZN A 29 NE2 HIS A 26 1555 1555 1.99
SITE 1 ZNB 4 CYS A 4 CYS A 9 HIS A 22 HIS A 26
SITE 1 BTD 1 NVA A 7
SITE 1 AC1 4 CYS A 4 CYS A 9 HIS A 22 HIS 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 - v 29 2 Bytes