Header list of 1yho.pdb file
Complete list - r 2 2 Bytes
HEADER OXIDOREDUCTASE 10-JAN-05 1YHO TITLE SOLUTION STRUCTURE OF HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH TITLE 2 TRIMETHOPRIM AND NADPH, 25 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NF1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMT702 KEYWDS DHFR, INHIBITOR-ENZYME COMPLEX, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 25 MDLTYP MINIMIZED AVERAGE AUTHOR V.I.POLSHAKOV,B.BIRDSALL REVDAT 3 02-MAR-22 1YHO 1 REMARK REVDAT 2 24-FEB-09 1YHO 1 VERSN REVDAT 1 22-NOV-05 1YHO 0 JRNL AUTH N.V.KOVALEVSKAYA,Y.D.SMURNYY,V.I.POLSHAKOV,B.BIRDSALL, JRNL AUTH 2 A.F.BRADBURY,T.FRENKIEL,J.FEENEY JRNL TITL SOLUTION STRUCTURE OF HUMAN DIHYDROFOLATE REDUCTASE IN ITS JRNL TITL 2 COMPLEX WITH TRIMETHOPRIM AND NADPH. JRNL REF J.BIOMOL.NMR V. 33 69 2005 JRNL REFN ISSN 0925-2738 JRNL PMID 16222560 JRNL DOI 10.1007/S10858-005-1475-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR VARIAN INC, CNS BRUNGER, ARIA REMARK 3 AUTHORS : 6.1 (VNMR), 1.1 (CNS), 2.0A (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HIGH TEMP (1000 K) STAGE: 30 PS (10000 SEPS), 1000 -> 0 K COOLING REMARK 3 (25 K STEP, 30PS TRAJECTORY ON EACH STEP). REMARK 3 700 STEPS OF FINAL ENERGY OPTIMIZATION. REMARK 4 REMARK 4 1YHO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031522. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : UNIFORM (RANDOM) LABELING WITH REMARK 210 13C, 15N AT KNOWN LABELING REMARK 210 LEVELS: U-95% 13C, U-98% 15N, 1 REMARK 210 MM; NADPH 1MM, TRIMETHOPRIME 1MM; REMARK 210 50MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D COSY; 15N-HSQC; 13C REMARK 210 -HSQC; 13C-NOESY-HSQC; 15N-NOESY- REMARK 210 HSQC; 15N-REJECTED-NOESY; 13C- REMARK 210 REJECTED-NOESY; HNCA; HNCO; REMARK 210 HN(CO)CA; HNCACB; CBCA(CO)NH; REMARK 210 HBHA(CO)NH; HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE DELAGLIO, SPARKY GODDARD REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: BACKBONE ASSIGMENT WAS PERFORMED USING TRIPLE-RESONANCE REMARK 210 NMR SPECTROSCOPY. 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 THR A 40 86.38 -68.87 REMARK 500 1 ASP A 110 -53.13 -124.47 REMARK 500 1 GLN A 140 140.08 -174.21 REMARK 500 2 PRO A 25 173.64 -53.11 REMARK 500 2 THR A 40 93.37 -67.97 REMARK 500 2 LEU A 67 94.19 -65.65 REMARK 500 2 VAL A 115 -67.21 -96.10 REMARK 500 2 GLN A 140 131.31 -171.41 REMARK 500 3 SER A 42 36.23 -98.71 REMARK 500 3 ASP A 110 -64.47 -130.98 REMARK 500 3 GLN A 140 124.05 -170.87 REMARK 500 4 THR A 40 79.15 -67.25 REMARK 500 4 SER A 42 36.69 -96.11 REMARK 500 4 ASP A 110 -68.47 -125.71 REMARK 500 4 VAL A 115 -65.88 -94.65 REMARK 500 4 GLN A 140 137.72 -171.42 REMARK 500 5 ASP A 110 -52.69 -130.09 REMARK 500 5 GLN A 140 124.19 -170.26 REMARK 500 6 LEU A 67 93.07 -62.88 REMARK 500 7 THR A 40 93.77 -68.34 REMARK 500 7 GLN A 140 124.48 -176.93 REMARK 500 8 GLN A 140 127.62 -174.40 REMARK 500 9 PRO A 25 -177.35 -55.61 REMARK 500 9 THR A 40 82.08 -68.74 REMARK 500 9 ASP A 110 -50.11 -138.72 REMARK 500 9 GLN A 140 135.48 -174.07 REMARK 500 10 ASP A 110 -57.16 -125.98 REMARK 500 10 GLN A 140 135.75 -176.97 REMARK 500 11 PRO A 25 172.83 -54.72 REMARK 500 11 THR A 40 94.32 -67.27 REMARK 500 11 VAL A 115 40.11 -109.01 REMARK 500 12 GLN A 140 123.88 -176.54 REMARK 500 13 PRO A 25 178.46 -53.97 REMARK 500 13 THR A 40 86.86 -68.94 REMARK 500 13 LEU A 67 93.87 -69.48 REMARK 500 14 THR A 40 87.44 -68.70 REMARK 500 14 LEU A 67 93.63 -64.40 REMARK 500 15 THR A 40 93.89 -68.14 REMARK 500 15 LEU A 67 96.17 -67.51 REMARK 500 15 ASP A 110 -53.82 -126.80 REMARK 500 16 THR A 40 95.01 -68.27 REMARK 500 16 GLN A 140 130.28 -174.48 REMARK 500 17 LEU A 67 98.30 -60.90 REMARK 500 17 ASP A 110 -67.39 -134.60 REMARK 500 17 VAL A 115 40.47 -108.70 REMARK 500 17 GLN A 140 135.22 -170.03 REMARK 500 18 PRO A 25 178.74 -56.40 REMARK 500 18 LEU A 67 98.89 -62.66 REMARK 500 18 VAL A 115 -66.12 -93.29 REMARK 500 19 GLN A 140 134.41 -172.44 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. 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 NDP A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRR A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KMS RELATED DB: PDB REMARK 900 HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6- ([5- REMARK 900 QUINOLYLAMINO]METHYL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3- D]PYRIMIDINE REMARK 900 (SRI-9439), A LIPOPHILIC ANTIFOLATE REMARK 900 RELATED ID: 1KMV RELATED DB: PDB REMARK 900 HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (Z)- 6-(2-[2, REMARK 900 5-DIMETHOXYPHENYL]ETHEN-1-YL)-2,4-DIAMINO-5- METHYLPYRIDO[2,3-D] REMARK 900 PYRIMIDINE (SRI-9662), A LIPOPHILIC ANTIFOLATE REMARK 900 RELATED ID: 1LUD RELATED DB: PDB REMARK 900 L.CASEI DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIMETHOPRIME AND REMARK 900 NADPH DBREF 1YHO A 1 186 UNP P00374 DYR_HUMAN 1 186 SEQRES 1 A 186 VAL GLY SER LEU ASN CYS ILE VAL ALA VAL SER GLN ASN SEQRES 2 A 186 MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO PRO SEQRES 3 A 186 LEU ARG ASN GLU PHE ARG TYR PHE GLN ARG MET THR THR SEQRES 4 A 186 THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE MET SEQRES 5 A 186 GLY LYS LYS THR TRP PHE SER ILE PRO GLU LYS ASN ARG SEQRES 6 A 186 PRO LEU LYS GLY ARG ILE ASN LEU VAL LEU SER ARG GLU SEQRES 7 A 186 LEU LYS GLU PRO PRO GLN GLY ALA HIS PHE LEU SER ARG SEQRES 8 A 186 SER LEU ASP ASP ALA LEU LYS LEU THR GLU GLN PRO GLU SEQRES 9 A 186 LEU ALA ASN LYS VAL ASP MET VAL TRP ILE VAL GLY GLY SEQRES 10 A 186 SER SER VAL TYR LYS GLU ALA MET ASN HIS PRO GLY HIS SEQRES 11 A 186 LEU LYS LEU PHE VAL THR ARG ILE MET GLN ASP PHE GLU SEQRES 12 A 186 SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLU LYS TYR SEQRES 13 A 186 LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER ASP VAL SEQRES 14 A 186 GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL TYR SEQRES 15 A 186 GLU LYS ASN ASP HET NDP A 190 74 HET TRR A 200 40 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM TRR 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 TRR C14 H19 N4 O3 1+ HELIX 1 1 LEU A 27 THR A 40 1 14 HELIX 2 2 LYS A 54 ILE A 60 1 7 HELIX 3 3 SER A 92 GLN A 102 1 11 HELIX 4 4 GLN A 102 ASN A 107 1 6 HELIX 5 5 GLY A 117 MET A 125 1 9 SHEET 1 A 8 PHE A 88 SER A 90 0 SHEET 2 A 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88 SHEET 3 A 8 GLN A 47 GLY A 53 1 N MET A 52 O LEU A 73 SHEET 4 A 8 VAL A 109 ILE A 114 1 O TRP A 113 N LEU A 49 SHEET 5 A 8 SER A 3 SER A 11 1 N ASN A 5 O ILE A 114 SHEET 6 A 8 LEU A 131 MET A 139 1 O THR A 136 N VAL A 10 SHEET 7 A 8 ILE A 175 LYS A 184 -1 O TYR A 182 N LEU A 133 SHEET 8 A 8 TYR A 156 LEU A 159 -1 N LEU A 159 O VAL A 181 SHEET 1 B 8 PHE A 88 SER A 90 0 SHEET 2 B 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88 SHEET 3 B 8 GLN A 47 GLY A 53 1 N MET A 52 O LEU A 73 SHEET 4 B 8 VAL A 109 ILE A 114 1 O TRP A 113 N LEU A 49 SHEET 5 B 8 SER A 3 SER A 11 1 N ASN A 5 O ILE A 114 SHEET 6 B 8 LEU A 131 MET A 139 1 O THR A 136 N VAL A 10 SHEET 7 B 8 ILE A 175 LYS A 184 -1 O TYR A 182 N LEU A 133 SHEET 8 B 8 GLN A 170 GLU A 172 -1 N GLU A 172 O ILE A 175 SHEET 1 C 2 GLY A 15 GLY A 17 0 SHEET 2 C 2 THR A 146 PHE A 147 -1 O THR A 146 N GLY A 17 CISPEP 1 ARG A 65 PRO A 66 1 -7.24 CISPEP 2 GLY A 116 GLY A 117 1 0.14 CISPEP 3 ARG A 65 PRO A 66 2 -7.86 CISPEP 4 GLY A 116 GLY A 117 2 0.17 CISPEP 5 ARG A 65 PRO A 66 3 -9.07 CISPEP 6 GLY A 116 GLY A 117 3 0.11 CISPEP 7 ARG A 65 PRO A 66 4 -5.77 CISPEP 8 GLY A 116 GLY A 117 4 0.25 CISPEP 9 ARG A 65 PRO A 66 5 -7.39 CISPEP 10 GLY A 116 GLY A 117 5 0.05 CISPEP 11 ARG A 65 PRO A 66 6 4.04 CISPEP 12 GLY A 116 GLY A 117 6 0.08 CISPEP 13 ARG A 65 PRO A 66 7 -8.86 CISPEP 14 GLY A 116 GLY A 117 7 0.23 CISPEP 15 ARG A 65 PRO A 66 8 -10.52 CISPEP 16 GLY A 116 GLY A 117 8 0.17 CISPEP 17 ARG A 65 PRO A 66 9 -4.57 CISPEP 18 GLY A 116 GLY A 117 9 0.07 CISPEP 19 ARG A 65 PRO A 66 10 -9.53 CISPEP 20 GLY A 116 GLY A 117 10 0.13 CISPEP 21 ARG A 65 PRO A 66 11 -9.57 CISPEP 22 GLY A 116 GLY A 117 11 0.13 CISPEP 23 ARG A 65 PRO A 66 12 -5.52 CISPEP 24 GLY A 116 GLY A 117 12 0.19 CISPEP 25 ARG A 65 PRO A 66 13 1.08 CISPEP 26 GLY A 116 GLY A 117 13 0.17 CISPEP 27 ARG A 65 PRO A 66 14 -3.17 CISPEP 28 GLY A 116 GLY A 117 14 0.18 CISPEP 29 ARG A 65 PRO A 66 15 5.56 CISPEP 30 GLY A 116 GLY A 117 15 0.21 CISPEP 31 ARG A 65 PRO A 66 16 -9.08 CISPEP 32 GLY A 116 GLY A 117 16 0.08 CISPEP 33 ARG A 65 PRO A 66 17 -3.70 CISPEP 34 GLY A 116 GLY A 117 17 0.20 CISPEP 35 ARG A 65 PRO A 66 18 -5.70 CISPEP 36 GLY A 116 GLY A 117 18 0.17 CISPEP 37 ARG A 65 PRO A 66 19 -8.59 CISPEP 38 GLY A 116 GLY A 117 19 0.14 CISPEP 39 ARG A 65 PRO A 66 20 -12.12 CISPEP 40 GLY A 116 GLY A 117 20 0.20 CISPEP 41 ARG A 65 PRO A 66 21 9.84 CISPEP 42 GLY A 116 GLY A 117 21 0.13 CISPEP 43 ARG A 65 PRO A 66 22 -3.08 CISPEP 44 GLY A 116 GLY A 117 22 0.17 CISPEP 45 ARG A 65 PRO A 66 23 -10.81 CISPEP 46 GLY A 116 GLY A 117 23 0.20 CISPEP 47 ARG A 65 PRO A 66 24 -12.33 CISPEP 48 GLY A 116 GLY A 117 24 0.32 CISPEP 49 ARG A 65 PRO A 66 25 -9.39 CISPEP 50 GLY A 116 GLY A 117 25 0.22 SITE 1 AC1 20 ALA A 9 ILE A 16 GLY A 17 LYS A 18 SITE 2 AC1 20 GLY A 20 LEU A 22 TRP A 24 GLY A 53 SITE 3 AC1 20 LYS A 54 LEU A 75 SER A 76 ARG A 77 SITE 4 AC1 20 ARG A 91 SER A 92 LEU A 93 GLY A 117 SITE 5 AC1 20 SER A 118 SER A 119 GLU A 123 TRR A 200 SITE 1 AC2 11 ILE A 7 VAL A 8 ALA A 9 LEU A 22 SITE 2 AC2 11 GLU A 30 PHE A 31 PHE A 34 ILE A 60 SITE 3 AC2 11 PRO A 61 VAL A 115 NDP A 190 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