Header list of 1f40.pdb file
Complete list - b 16 2 Bytes
HEADER ISOMERASE 07-JUN-00 1F40
TITLE SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC
TITLE 2 LIGAND
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FK506 BINDING PROTEIN (FKBP12);
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: PROTEIN COORDINATES WERE TAKEN FROM THE CRYSTAL
COMPND 6 STRUCTURE BY HOLT ET AL. (1993, PDB ACCESSION CODE 1FKG).
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 ORGAN: BRAIN;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PARS-3
KEYWDS ISOMERASE
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR C.SICH,S.IMPROTA,D.J.COWLEY,C.GUENET,J.P.MERLY,M.TEUFEL,V.SAUDEK
REVDAT 3 16-FEB-22 1F40 1 REMARK
REVDAT 2 24-FEB-09 1F40 1 VERSN
REVDAT 1 08-NOV-00 1F40 0
JRNL AUTH C.SICH,S.IMPROTA,D.J.COWLEY,C.GUENET,J.P.MERLY,M.TEUFEL,
JRNL AUTH 2 V.SAUDEK
JRNL TITL SOLUTION STRUCTURE OF A NEUROTROPHIC LIGAND BOUND TO FKBP12
JRNL TITL 2 AND ITS EFFECTS ON PROTEIN DYNAMICS.
JRNL REF EUR.J.BIOCHEM. V. 267 5342 2000
JRNL REFN ISSN 0014-2956
JRNL PMID 10951192
JRNL DOI 10.1046/J.1432-1327.2000.01551.X
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.P.STEINER,G.S.HAMILTON,D.T.ROSS,H.L.VALENTINE,H.GUO,
REMARK 1 AUTH 2 M.A.CONNOLLY,S.LIANG,C.RAMSEY,J.H.LI,W.HUANG,P.HOWORTH,
REMARK 1 AUTH 3 R.SONI,M.FULLER,H.SAUER,A.C.NOWOTNIK,P.D.SUZDAK
REMARK 1 TITL NEUROTROPHIC IMMUNOPHILIN LIGANDS STIMULATE STRUCTURAL AND
REMARK 1 TITL 2 FUNCTIONAL RECOVERY IN NEURODEGENERATIVE ANIMAL MODELS
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 94 2019 1997
REMARK 1 REFN ISSN 0027-8424
REMARK 1 DOI 10.1073/PNAS.94.5.2019
REMARK 1 REFERENCE 2
REMARK 1 AUTH G.D.VAN DUYNE,R.F.STAENDERT,P.A.KARPLUS,S.L.SCHREIBER,
REMARK 1 AUTH 2 J.CLARDY
REMARK 1 TITL ATOMIC STRUCTURE OF FKBP-FK506, AN
REMARK 1 TITL 2 IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
REMARK 1 REF SCIENCE V. 252 839 1991
REMARK 1 REFN ISSN 0036-8075
REMARK 1 REFERENCE 3
REMARK 1 AUTH D.A.HOLT,J.I.LUENGO,D.S.YAMASHITA,H.-J.OH,A.L.KONALIAN,
REMARK 1 AUTH 2 H.-K.YEN,L.W.ROZAMUS,M.BRANDT,M.J.BOSSARD,M.A.LEVY,
REMARK 1 AUTH 3 D.S.EGGLESTON,J.LIAN,L.W.SCHULTZ,T.J.STOUT,J.CLARDY
REMARK 1 TITL DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY
REMARK 1 TITL 2 FKBP LIGANDS AND THE X-RAY STRUCTURE OF THEIR COMPLEXES WITH
REMARK 1 TITL 3 FKBP12
REMARK 1 REF J.AM.CHEM.SOC. V. 115 9925 1993
REMARK 1 REFN ISSN 0002-7863
REMARK 1 REFERENCE 4
REMARK 1 AUTH J.W.CHENG,C.A.LEPRE,J.M.MOORE
REMARK 1 TITL 15N NMR RELAXATION STUDIES OF THE FK506 BINDING PROTEIN:
REMARK 1 TITL 2 DYNAMIC EFFECTS OF LIGAND BINDING AND IMPLICATIONS FOR
REMARK 1 TITL 3 CALCINERIN INHIBITION
REMARK 1 REF BIOCHEMISTRY V. 33 4093 1994
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 1.1, X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER A. (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING A
REMARK 3 TOTAL OF 50 LIGAND-LIGAND AND 18 PROTEIN-LIGAND DISTANCE
REMARK 3 RESTRAINTS. NOES INVOLVING DEGENERATE PROTONS WERE INCORPORATED
REMARK 3 AS AMBIGUOUS RESTRAINTS.
REMARK 4
REMARK 4 1F40 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-00.
REMARK 100 THE DEPOSITION ID IS D_1000011214.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 100MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.5 MM FKBP12 U-15N; 100 MM
REMARK 210 PHOSPHATE BUFFER; 0.01% NAN3;
REMARK 210 0.5 MM FKBP12 U-15N; 1MM GPI-
REMARK 210 1046; 100 MM PHOSPHATE BUFFER;
REMARK 210 0.01% NAN3; 2MM FKBP12 U-15N,13C;
REMARK 210 2MM GPI-1046; 100 MM PHOSPHATE
REMARK 210 BUFFER; 0.01% NAN3
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY;
REMARK 210 2D_15N,13C-FILTERED NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 1.1, AURELIA 2.1, FELIX
REMARK 210 97.2
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH FAVORABLE NON-BOND ENERGY,
REMARK 210 STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
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: 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 1 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 2 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 2 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 2 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 2 VAL A 101 CG1 - CB - CG2 ANGL. DEV. = -9.6 DEGREES
REMARK 500 3 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 3 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 3 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 3 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 3 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 3 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 4 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 4 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 4 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 4 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 4 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 4 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 4 TYR A 80 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 5 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 5 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 5 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 5 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 5 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 5 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES
REMARK 500 6 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 6 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 6 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 6 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 6 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 6 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES
REMARK 500 7 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 7 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 7 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 7 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 7 TRP A 59 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 7 TRP A 59 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES
REMARK 500 7 VAL A 101 CG1 - CB - CG2 ANGL. DEV. = -9.6 DEGREES
REMARK 500 8 ARG A 18 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 8 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 8 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 8 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 66 ANGLE DEVIATIONS.
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 ALA A 81 -116.39 -137.74
REMARK 500 2 ALA A 81 -116.55 -137.86
REMARK 500 3 ALA A 81 -116.60 -137.90
REMARK 500 4 ALA A 81 -116.58 -137.83
REMARK 500 5 ALA A 81 -116.60 -137.86
REMARK 500 6 ALA A 81 -116.54 -137.79
REMARK 500 7 ALA A 81 -116.62 -137.79
REMARK 500 8 ALA A 81 -116.52 -137.64
REMARK 500 9 ALA A 81 -116.51 -137.76
REMARK 500 10 ALA A 81 -116.53 -137.82
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 GPI A 108
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1FKJ RELATED DB: PDB
REMARK 900 1FKG CONTAINS THE SAME PROTEIN COMPLEXED WITH FK506
REMARK 900 RELATED ID: 1FKG RELATED DB: PDB
REMARK 900 1FKG CONTAINS THE SAME PROTEIN COMPLEXED WITH A NON-MACROCYCLIC
REMARK 900 FK506 ANALOGUE
DBREF 1F40 A 1 107 UNP P62942 FKB1A_HUMAN 2 108
SEQRES 1 A 107 GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG
SEQRES 2 A 107 THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR
SEQRES 3 A 107 THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER
SEQRES 4 A 107 ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS
SEQRES 5 A 107 GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN
SEQRES 6 A 107 MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO
SEQRES 7 A 107 ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE
SEQRES 8 A 107 PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU
SEQRES 9 A 107 LYS LEU GLU
HET GPI A 108 54
HETNAM GPI (2S)-[3-PYRIDYL-1-PROPYL]-1-[3,3-DIMETHYL-1,2-
HETNAM 2 GPI DIOXOPENTYL]-2-PYRROLIDINECARBOXYLATE
HETSYN GPI GPI-1046
FORMUL 2 GPI C20 H28 N2 O4
HELIX 1 1 SER A 39 ASN A 43 1 5
HELIX 2 2 ILE A 56 ALA A 64 1 9
HELIX 3 3 PRO A 78 ALA A 81 5 4
SHEET 1 A 5 VAL A 2 SER A 8 0
SHEET 2 A 5 ARG A 71 ILE A 76 -1 O ARG A 71 N ILE A 7
SHEET 3 A 5 LEU A 97 GLU A 107 -1 O LEU A 97 N ILE A 76
SHEET 4 A 5 THR A 21 LEU A 30 -1 O THR A 21 N GLU A 107
SHEET 5 A 5 LYS A 35 SER A 38 -1 N PHE A 36 O GLY A 28
SHEET 1 B 5 VAL A 2 SER A 8 0
SHEET 2 B 5 ARG A 71 ILE A 76 -1 O ARG A 71 N ILE A 7
SHEET 3 B 5 LEU A 97 GLU A 107 -1 O LEU A 97 N ILE A 76
SHEET 4 B 5 THR A 21 LEU A 30 -1 O THR A 21 N GLU A 107
SHEET 5 B 5 PHE A 46 MET A 49 -1 N PHE A 46 O VAL A 24
SITE 1 AC1 7 TYR A 26 PHE A 46 GLU A 54 VAL A 55
SITE 2 AC1 7 ILE A 56 TYR A 82 HIS A 87
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 - b 16 2 Bytes