HEADER CELL CYCLE 23-MAY-16 5L3M
TITLE D11 BOUND [S39_PQ]-IGF-II
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INSULIN-LIKE GROWTH FACTOR II;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: IGF-II,SOMATOMEDIN-A,T3M-11-DERIVED GROWTH FACTOR;
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 GENE: IGF2, PP1446;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS IGF-II, CELL CYCLE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR R.HEXNEROVA
REVDAT 5 14-JUN-23 5L3M 1 REMARK
REVDAT 4 08-MAY-19 5L3M 1 REMARK
REVDAT 3 19-OCT-16 5L3M 1 JRNL
REVDAT 2 24-AUG-16 5L3M 1 JRNL
REVDAT 1 10-AUG-16 5L3M 0
JRNL AUTH R.HEXNEROVA,K.KRIZKOVA,M.FABRY,I.SIEGLOVA,K.KEDROVA,
JRNL AUTH 2 M.COLLINSOVA,P.ULLRICHOVA,P.SRB,C.WILLIAMS,M.P.CRUMP,
JRNL AUTH 3 Z.TOSNER,J.JIRACEK,V.VEVERKA,L.ZAKOVA
JRNL TITL PROBING RECEPTOR SPECIFICITY BY SAMPLING THE CONFORMATIONAL
JRNL TITL 2 SPACE OF THE INSULIN-LIKE GROWTH FACTOR II C-DOMAIN.
JRNL REF J.BIOL.CHEM. V. 291 21234 2016
JRNL REFN ESSN 1083-351X
JRNL PMID 27510031
JRNL DOI 10.1074/JBC.M116.741041
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : YASARA
REMARK 3 AUTHORS : HOEGENAUER, KORAIMANN, KUNGL, VRIEND
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5L3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-16.
REMARK 100 THE DEPOSITION ID IS D_1200000059.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 4.2
REMARK 210 IONIC STRENGTH : 0
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 20 MM D4 ACETIC ACID, 90%
REMARK 210 H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH;
REMARK 210 3D HNCACB; 3D HNCO; 3D HN(CA)CO;
REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY;
REMARK 210 3D 1H-13C NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE III
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
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: 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 5660 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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: 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: 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 24 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 ASP A 15 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 8 ASP A 15 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 15 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 18 ASP A 15 CB - CG - OD1 ANGL. DEV. = 5.7 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 CYS A 9 -47.01 -132.51
REMARK 500 1 SER A 33 -171.34 60.76
REMARK 500 1 ARG A 34 21.71 -146.17
REMARK 500 2 SER A 5 38.49 -96.28
REMARK 500 2 CYS A 21 -53.85 -137.18
REMARK 500 2 SER A 33 -167.03 52.56
REMARK 500 2 ARG A 34 38.51 -149.31
REMARK 500 2 ARG A 38 18.39 57.90
REMARK 500 3 CYS A 9 -56.78 -123.19
REMARK 500 3 SER A 33 29.59 -75.44
REMARK 500 3 SER A 39 70.22 50.78
REMARK 500 3 SER A 68 40.34 -85.88
REMARK 500 4 CYS A 9 -164.89 -112.98
REMARK 500 4 CYS A 21 29.91 -150.30
REMARK 500 4 ARG A 37 -178.44 52.33
REMARK 500 4 SER A 39 151.98 75.63
REMARK 500 4 LYS A 67 45.47 -76.52
REMARK 500 5 ASP A 23 15.09 -66.71
REMARK 500 5 ARG A 38 43.89 -76.70
REMARK 500 5 SER A 39 77.22 38.28
REMARK 500 5 LYS A 67 47.20 -81.31
REMARK 500 6 SER A 33 49.28 -77.12
REMARK 500 6 ARG A 38 17.84 58.52
REMARK 500 6 LYS A 67 30.78 -92.01
REMARK 500 7 CYS A 9 -34.33 -133.87
REMARK 500 7 ARG A 34 48.45 -74.67
REMARK 500 7 SER A 36 47.42 -70.69
REMARK 500 7 ARG A 37 34.94 -78.63
REMARK 500 7 SER A 39 155.06 71.70
REMARK 500 9 ARG A 30 156.25 67.65
REMARK 500 9 SER A 33 -149.03 53.27
REMARK 500 10 SER A 5 36.90 -156.30
REMARK 500 10 CYS A 9 -168.98 -127.31
REMARK 500 10 SER A 33 -164.74 57.83
REMARK 500 10 ARG A 34 23.03 -145.82
REMARK 500 10 LYS A 67 45.52 -83.45
REMARK 500 11 CYS A 21 29.95 -158.90
REMARK 500 11 ARG A 30 165.37 68.75
REMARK 500 11 SER A 33 94.98 -55.57
REMARK 500 12 ASP A 23 8.89 -65.35
REMARK 500 12 SER A 33 -155.20 57.20
REMARK 500 12 ARG A 38 22.62 -77.53
REMARK 500 12 LYS A 67 27.43 -77.77
REMARK 500 13 CYS A 21 27.59 -158.81
REMARK 500 13 SER A 33 -165.50 59.55
REMARK 500 13 ARG A 34 39.32 -153.44
REMARK 500 13 SER A 39 150.78 74.54
REMARK 500 14 SER A 5 117.48 -175.85
REMARK 500 14 GLU A 6 -77.09 -142.95
REMARK 500 15 ASP A 23 3.62 -66.29
REMARK 500
REMARK 500 THIS ENTRY HAS 79 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 34001 RELATED DB: BMRB
DBREF 5L3M A 1 69 UNP P01344 IGF2_HUMAN 25 91
SEQADV 5L3M PRO A 40 UNP P01344 INSERTION
SEQADV 5L3M GLN A 41 UNP P01344 INSERTION
SEQRES 1 A 69 ALA TYR ARG PRO SER GLU THR LEU CYS GLY GLY GLU LEU
SEQRES 2 A 69 VAL ASP THR LEU GLN PHE VAL CYS GLY ASP ARG GLY PHE
SEQRES 3 A 69 TYR PHE SER ARG PRO ALA SER ARG VAL SER ARG ARG SER
SEQRES 4 A 69 PRO GLN ARG GLY ILE VAL GLU GLU CYS CYS PHE ARG SER
SEQRES 5 A 69 CYS ASP LEU ALA LEU LEU GLU THR TYR CYS ALA THR PRO
SEQRES 6 A 69 ALA LYS SER GLU
HELIX 1 AA1 GLY A 10 GLY A 22 1 13
HELIX 2 AA2 ASP A 23 GLY A 25 5 3
HELIX 3 AA3 GLY A 43 CYS A 49 1 7
HELIX 4 AA4 ASP A 54 GLU A 59 1 6
HELIX 5 AA5 THR A 60 CYS A 62 5 3
SSBOND 1 CYS A 9 CYS A 49 1555 1555 2.03
SSBOND 2 CYS A 21 CYS A 62 1555 1555 2.03
SSBOND 3 CYS A 48 CYS A 53 1555 1555 2.03
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
(ATOM LINES ARE NOT SHOWN.)
END
