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PDBsum entry 3irl

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Carbohydrate PDB id
3irl
Jmol
Contents
Ligands
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS-
SGN-IDS-SGN-IDS
HEADER    CARBOHYDRATE                            24-AUG-09   3IRL
TITLE     SOLUTION STRUCTURE OF HEPARIN DP36
CAVEAT     3IRL    POOR INTRAMOLECULAR CONTACTS IN ALL 14 MODELS ARE DUE TO THE
CAVEAT   2 3IRL     ALGORITHM IN USE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SUGAR (36-MER);
COMPND   3 CHAIN: A;
COMPND   4 OTHER_DETAILS: HEPARIN DP36
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE   3 ORGANISM_TAXID: 9913;
SOURCE   4 STRAIN: BOVINE LUNG HEPARIN DP36 WAS PURIFIED AFTER DIGESTION  WITH
SOURCE   5 HEPARINASE I.
KEYWDS    OLIGOSACCHARIDE, X-RAY SCATTERING, CARBOHYDRATE
EXPDTA    SOLUTION SCATTERING
NUMMDL    14
AUTHOR    S.KHAN,J.GOR,B.MULLOY,S.J.PERKINS
REVDAT   3   13-JUL-11 3IRL    1       VERSN
REVDAT   2   07-APR-10 3IRL    1       REMARK
REVDAT   1   03-NOV-09 3IRL    0
JRNL        AUTH   S.KHAN,J.GOR,B.MULLOY,S.J.PERKINS
JRNL        TITL   SEMI-RIGID SOLUTION STRUCTURES OF HEPARIN BY CONSTRAINED
JRNL        TITL 2 X-RAY SCATTERING MODELLING: NEW INSIGHT INTO HEPARIN-PROTEIN
JRNL        TITL 3 COMPLEXES.
JRNL        REF    J.MOL.BIOL.                   V. 395   504 2010
JRNL        REFN                   ISSN 0022-2836
JRNL        PMID   19895822
JRNL        DOI    10.1016/J.JMB.2009.10.064
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : INSIGHT II 98, DISCOVERY STUDIO 2.1
REMARK   3   AUTHORS     :
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 0
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 630
REMARK   3   SOLVENT ATOMS            : 0
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3IRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-09.
REMARK 100 THE RCSB ID CODE IS RCSB054777.
REMARK 265
REMARK 265 EXPERIMENTAL DETAILS
REMARK 265
REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING
REMARK 265  DATA ACQUISITION
REMARK 265   RADIATION/NEUTRON SOURCE                 : ESRF GRENOBLE
REMARK 265   SYNCHROTRON (Y/N)                        : Y
REMARK 265   BEAMLINE TYPE                            : IDO2
REMARK 265   BEAMLINE INSTRUMENT                      : NULL
REMARK 265   DETECTOR TYPE                            : FRELON CCD CAMERA
REMARK 265   DETECTOR MANUFACTURER DETAILS            : NULL
REMARK 265   TEMPERATURE (KELVIN)                     : 293
REMARK 265   PH                                       : 7.4
REMARK 265   NUMBER OF TIME FRAMES USED               : 10
REMARK 265   PROTEIN CONCENTRATION RANGE (MG/ML)      : 0.50
REMARK 265   SAMPLE BUFFER                            : 137 MM NACL 10 MM
REMARK 265                                              HEPES
REMARK 265   DATA REDUCTION SOFTWARE                  : MULTICCD
REMARK 265   GUINIER MEAN RADIUS OF GYRATION (NM)     : 3.12
REMARK 265   SIGMA MEAN RADIUS OF GYRATION            : 0.10
REMARK 265   R(XS-1) MEAN CROSS SECTIONAL RADII (NM)  : 0.53
REMARK 265   R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : 0.01
REMARK 265   R(XS-2) MEAN CROSS SECTIONAL RADII (NM)  : NULL
REMARK 265   R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL
REMARK 265   P(R) PROTEIN LENGTH (NM)                 : 0.5
REMARK 265
REMARK 265 DATA ANALYSIS AND MODEL FITTING:
REMARK 265  METHOD USED TO DETERMINE THE STRUCTURE: CONSTRAINED SCATTERING
REMARK 265                                          MODELLING
REMARK 265  SOFTWARE USED    : INSIGHT II, DISCOVERY STUDIO, SCTPL7, GNOM
REMARK 265  SOFTWARE AUTHORS : NULL
REMARK 265  STARTING MODEL   : NULL
REMARK 265
REMARK 265 CONFORMERS, NUMBER CALCULATED   : 5000
REMARK 265 CONFORMERS, NUMBER SUBMITTED    : 14
REMARK 265 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST
REMARK 265  GOODNESS-OF-FIT R-FACTOR AFTER FILTERING ON RG
REMARK 265
REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 265
REMARK 265  OTHER DETAILS: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
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   C3   IDS A     4     O1S  SGN A     5              0.66
REMARK 500   O3   IDS A     4     O1S  SGN A     5              1.22
REMARK 500   O2   IDS A    30     O3S  SGN A    31              1.25
REMARK 500   O4S  SGN A    27     O1S  IDS A    28              1.28
REMARK 500   O3   IDS A    10     O1S  SGN A    11              1.39
REMARK 500   O5S  SGN A    23     O62  IDS A    24              1.45
REMARK 500   O4S  SGN A    31     O1S  IDS A    32              1.52
REMARK 500   O3S  IDS A    24     O3S  SGN A    25              1.53
REMARK 500   O3   IDS A    22     O3S  SGN A    23              1.54
REMARK 500   C2   IDS A     4     O1S  SGN A     5              1.57
REMARK 500   O4S  SGN A    17     O1S  IDS A    18              1.59
REMARK 500   O3   IDS A     2     O3S  SGN A     3              1.60
REMARK 500   O3   IDS A    30     O1S  SGN A    31              1.65
REMARK 500   O3   IDS A    24     O3S  SGN A    25              1.65
REMARK 500   O3   IDS A    24     O1S  SGN A    25              1.70
REMARK 500   O3   IDS A    22     N    SGN A    23              1.75
REMARK 500   O3   IDS A    24     S1   SGN A    25              1.76
REMARK 500   O5S  SGN A    23     C6   IDS A    24              1.78
REMARK 500   O2   IDS A    24     O3S  SGN A    25              1.82
REMARK 500   O3   IDS A     2     O1S  SGN A     3              1.85
REMARK 500   O3   IDS A    10     S1   SGN A    11              1.88
REMARK 500   C3   IDS A    24     N    SGN A    25              1.89
REMARK 500   O3   IDS A     2     S1   SGN A     3              1.89
REMARK 500   C6   SGN A    17     O2S  IDS A    18              1.90
REMARK 500   C3   IDS A     4     S1   SGN A     5              1.90
REMARK 500   O3   IDS A    26     O3S  SGN A    27              1.91
REMARK 500   C6   SGN A    31     O2S  IDS A    32              1.92
REMARK 500   O3   SGN A    33     C5   IDS A    34              1.94
REMARK 500   S    IDS A    24     O3S  SGN A    25              1.94
REMARK 500   O2   IDS A     4     O1S  SGN A     5              2.01
REMARK 500   O6   SGN A    23     O5   IDS A    24              2.02
REMARK 500   O3   IDS A    22     S1   SGN A    23              2.02
REMARK 500   O2   IDS A     4     O3S  SGN A     5              2.02
REMARK 500   O3   IDS A    26     O1S  SGN A    27              2.02
REMARK 500   O3   SGN A    33     C6   IDS A    34              2.02
REMARK 500   O5S  SGN A    29     O62  IDS A    30              2.04
REMARK 500   O6   SGN A    29     O5   IDS A    30              2.07
REMARK 500   O3   IDS A    26     S1   SGN A    27              2.09
REMARK 500   O4S  SGN A    17     S    IDS A    18              2.10
REMARK 500   O3   IDS A    20     O3S  SGN A    21              2.11
REMARK 500   C2   IDS A    30     O3S  SGN A    31              2.11
REMARK 500   S2   SGN A    23     O62  IDS A    24              2.11
REMARK 500   O5S  SGN A    23     O5   IDS A    24              2.13
REMARK 500   O5S  SGN A    23     C5   IDS A    24              2.14
REMARK 500   C3   IDS A    24     O3S  SGN A    25              2.16
REMARK 500   C3   IDS A    30     N    SGN A    31              2.16
REMARK 500   O4S  SGN A    17     O2S  IDS A    18              2.16
REMARK 500   C3   IDS A    22     N    SGN A    23              2.17
REMARK 500   C5   SGN A    27     O2S  IDS A    28              2.19
REMARK 500   C4   IDS A     4     O1S  SGN A     5              2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HPN   RELATED DB: PDB
REMARK 900 N.M.R. AND MOLECULAR-MODELLING STUDIES OF THE SOLUTION
REMARK 900 CONFORMATION OF HEPARIN
REMARK 900 RELATED ID: 3IRI   RELATED DB: PDB
REMARK 900 RELATED ID: 3IRJ   RELATED DB: PDB
REMARK 900 RELATED ID: 3IRK   RELATED DB: PDB
SEQRES   1 A   36  SGN IDS SGN IDS SGN IDS SGN IDS SGN IDS SGN IDS SGN
SEQRES   2 A   36  IDS SGN IDS SGN IDS SGN IDS SGN IDS SGN IDS SGN IDS
SEQRES   3 A   36  SGN IDS SGN IDS SGN IDS SGN IDS SGN IDS
HET    SGN  A   1      19
HET    IDS  A   2      16
HET    SGN  A   3      19
HET    IDS  A   4      16
HET    SGN  A   5      19
HET    IDS  A   6      16
HET    SGN  A   7      19
HET    IDS  A   8      16
HET    SGN  A   9      19
HET    IDS  A  10      16
HET    SGN  A  11      19
HET    IDS  A  12      16
HET    SGN  A  13      19
HET    IDS  A  14      16
HET    SGN  A  15      19
HET    IDS  A  16      16
HET    SGN  A  17      19
HET    IDS  A  18      16
HET    SGN  A  19      19
HET    IDS  A  20      16
HET    SGN  A  21      19
HET    IDS  A  22      16
HET    SGN  A  23      19
HET    IDS  A  24      16
HET    SGN  A  25      19
HET    IDS  A  26      16
HET    SGN  A  27      19
HET    IDS  A  28      16
HET    SGN  A  29      19
HET    IDS  A  30      16
HET    SGN  A  31      19
HET    IDS  A  32      16
HET    SGN  A  33      19
HET    IDS  A  34      16
HET    SGN  A  35      19
HET    IDS  A  36      16
HETNAM     SGN N,O6-DISULFO-GLUCOSAMINE
HETNAM     IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
HETSYN     IDS O2-SULFO-GLUCURONIC ACID
FORMUL   1  SGN    18(C6 H13 N O11 S2)
FORMUL   1  IDS    18(C6 H10 O10 S)
LINK         C4  IDS A  10                 O1  SGN A  11     1555   1555  1.42
LINK         C4  SGN A  13                 O1  IDS A  14     1555   1555  1.42
LINK         C4  SGN A   1                 O1  IDS A   2     1555   1555  1.42
LINK         C4  SGN A  17                 O1  IDS A  18     1555   1555  1.42
LINK         C4  SGN A   7                 O1  IDS A   8     1555   1555  1.42
LINK         C4  SGN A  27                 O1  IDS A  28     1555   1555  1.42
LINK         C4  SGN A  31                 O1  IDS A  32     1555   1555  1.42
LINK         C4  IDS A  16                 O1  SGN A  17     1555   1555  1.42
LINK         C4  SGN A   5                 O1  IDS A   6     1555   1555  1.42
LINK         C4  IDS A  20                 O1  SGN A  21     1555   1555  1.42
LINK         C4  SGN A  23                 O1  IDS A  24     1555   1555  1.42
LINK         C4  IDS A  30                 O1  SGN A  31     1555   1555  1.42
LINK         C4  SGN A  29                 O1  IDS A  30     1555   1555  1.42
LINK         C4  SGN A  21                 O1  IDS A  22     1555   1555  1.42
LINK         C4  SGN A   3                 O1  IDS A   4     1555   1555  1.42
LINK         C4  SGN A  33                 O1  IDS A  34     1555   1555  1.42
LINK         C4  SGN A  35                 O1  IDS A  36     1555   1555  1.42
LINK         C4  SGN A  19                 O1  IDS A  20     1555   1555  1.42
LINK         C4  SGN A   9                 O1  IDS A  10     1555   1555  1.42
LINK         C4  IDS A  26                 O1  SGN A  27     1555   1555  1.42
LINK         C4  IDS A   6                 O1  SGN A   7     1555   1555  1.42
LINK         C4  IDS A   8                 O1  SGN A   9     1555   1555  1.42
LINK         C4  SGN A  11                 O1  IDS A  12     1555   1555  1.42
LINK         C4  SGN A  15                 O1  IDS A  16     1555   1555  1.42
LINK         C4  IDS A  28                 O1  SGN A  29     1555   1555  1.42
LINK         C4  SGN A  25                 O1  IDS A  26     1555   1555  1.42
LINK         C4  IDS A  18                 O1  SGN A  19     1555   1555  1.42
LINK         C4  IDS A  22                 O1  SGN A  23     1555   1555  1.42
LINK         C4  IDS A  34                 O1  SGN A  35     1555   1555  1.42
LINK         C4  IDS A   2                 O1  SGN A   3     1555   1555  1.42
LINK         C4  IDS A  24                 O1  SGN A  25     1555   1555  1.42
LINK         C4  IDS A  32                 O1  SGN A  33     1555   1555  1.42
LINK         C4  IDS A  12                 O1  SGN A  13     1555   1555  1.42
LINK         C4  IDS A  14                 O1  SGN A  15     1555   1555  1.42
LINK         C4  IDS A   4                 O1  SGN A   5     1555   1555  1.42
LINK         C6  SGN A  27                 O2S IDS A  28     1555   1555  1.50
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
      
 References