10 20 30 40 50 60 70 80 1F40 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ISOMERASE 07-JUN-00 1F40
TITLE SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A TITLE 2 NEUROTROPHIC 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 COMPND 6 CRYSTAL STRUCTURE BY HOLT ET AL. (1993, PDB ACCESSION CODE COMPND 7 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, AUTHOR 2 V.SAUDEK
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, JRNL AUTH 2 M.TEUFEL,V.SAUDEK JRNL TITL SOLUTION STRUCTURE OF A NEUROTROPHIC LIGAND BOUND JRNL TITL 2 TO FKBP12 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, REMARK 1 AUTH 2 H.GUO,M.A.CONNOLLY,S.LIANG,C.RAMSEY,J.H.LI,W.HUANG, REMARK 1 AUTH 3 P.HOWORTH,R.SONI,M.FULLER,H.SAUER,A.C.NOWOTNIK, REMARK 1 AUTH 4 P.D.SUZDAK REMARK 1 TITL NEUROTROPHIC IMMUNOPHILIN LIGANDS STIMULATE REMARK 1 TITL 2 STRUCTURAL AND FUNCTIONAL RECOVERY IN REMARK 1 TITL 3 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, REMARK 1 AUTH 2 S.L.SCHREIBER,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, REMARK 1 AUTH 2 A.L.KONALIAN,H.-K.YEN,L.W.ROZAMUS,M.BRANDT, REMARK 1 AUTH 3 M.J.BOSSARD,M.A.LEVY,D.S.EGGLESTON,J.LIAN, REMARK 1 AUTH 4 L.W.SCHULTZ,T.J.STOUT,J.CLARDY REMARK 1 TITL DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF REMARK 1 TITL 2 HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY STRUCTURE REMARK 1 TITL 3 OF THEIR COMPLEXES WITH 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 REMARK 1 TITL 2 PROTEIN: DYNAMIC EFFECTS OF LIGAND BINDING AND REMARK 1 TITL 3 IMPLICATIONS FOR 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 : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER A. 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 REMARK 3 INCORPORATED 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 RCSB ID CODE IS RCSB011214.
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, REMARK 210 13C; 2MM GPI-1046; 100 MM REMARK 210 PHOSPHATE BUFFER; 0.01% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 2D_ REMARK 210 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, REMARK 210 FELIX 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 REMARK 210 ENERGY,STRUCTURES WITH THE REMARK 210 LEAST 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 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. = -3.6 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. = -3.6 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- REMARK 900 MACROCYCLIC 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