PDB Short entry for 3IRK HEADER CARBOHYDRATE 24-AUG-09 3IRK TITLE SOLUTION STRUCTURE OF HEPARIN DP30 CAVEAT 3IRK POOR INTRAMOLECULAR CONTACTS IN ALL 14 MODELS ARE DUE TO THE CAVEAT 2 3IRK ALGORITHM IN USE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O- COMPND 3 SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L- COMPND 4 IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- COMPND 5 GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2- COMPND 6 DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO- COMPND 7 ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)- COMPND 8 ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1- COMPND 9 4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O- COMPND 10 SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2- COMPND 11 (SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L- COMPND 12 IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- COMPND 13 GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2- COMPND 14 DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO- COMPND 15 ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)- COMPND 16 ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1- COMPND 17 4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O- COMPND 18 SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2- COMPND 19 (SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L- COMPND 20 IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- COMPND 21 GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2- COMPND 22 DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO- COMPND 23 ALPHA-L-IDOPYRANURONIC ACID-(1-4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)- COMPND 24 ALPHA-D-GLUCOPYRANOSE-(1-4)-2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID-(1- COMPND 25 4)-2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE; COMPND 26 CHAIN: A; COMPND 27 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS OLIGOSACCHARIDE, X-RAY SCATTERING, CARBOHYDRATE EXPDTA SOLUTION SCATTERING NUMMDL 14 AUTHOR S.KHAN,J.GOR,B.MULLOY,S.J.PERKINS REVDAT 5 21-FEB-24 3IRK 1 HETSYN REVDAT 4 29-JUL-20 3IRK 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 ATOM REVDAT 3 13-JUL-11 3IRK 1 VERSN REVDAT 2 07-APR-10 3IRK 1 REMARK REVDAT 1 03-NOV-09 3IRK 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 : 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 : 525 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IRK 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 DEPOSITION ID IS D_1000054776. 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) : 2.83 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.14 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : 0.52 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 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: UNKNOWN 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 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 O3 IDS A 6 O1S SGN A 7 0.13 REMARK 500 O4S SGN A 15 O2S IDS A 16 0.47 REMARK 500 O3 IDS A 24 O1S SGN A 25 0.97 REMARK 500 O4S SGN A 15 S IDS A 16 1.20 REMARK 500 C3 IDS A 6 O1S SGN A 7 1.45 REMARK 500 O3 IDS A 6 S1 SGN A 7 1.53 REMARK 500 C3 IDS A 8 O1S SGN A 9 1.58 REMARK 500 S2 SGN A 15 O2S IDS A 16 1.60 REMARK 500 O5S SGN A 25 O6B IDS A 26 1.63 REMARK 500 O3 IDS A 22 O1S SGN A 23 1.83 REMARK 500 O2 IDS A 6 O3S SGN A 7 1.85 REMARK 500 O3 SGN A 7 O6B IDS A 8 1.86 REMARK 500 O3 IDS A 8 O1S SGN A 9 1.90 REMARK 500 O4S SGN A 15 O1S IDS A 16 1.95 REMARK 500 O3 IDS A 10 O1S SGN A 11 1.96 REMARK 500 C3 IDS A 6 S1 SGN A 7 1.97 REMARK 500 O5S SGN A 1 O5 IDS A 2 1.98 REMARK 500 O2 IDS A 10 O3S SGN A 11 1.99 REMARK 500 O2 IDS A 24 O3S SGN A 25 2.01 REMARK 500 C3 IDS A 24 O1S SGN A 25 2.01 REMARK 500 O3 IDS A 24 S1 SGN A 25 2.02 REMARK 500 C3 IDS A 6 N2 SGN A 7 2.05 REMARK 500 C3 IDS A 10 N2 SGN A 11 2.10 REMARK 500 C6 SGN A 9 O2S IDS A 10 2.10 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 CONFORMATION REMARK 900 OF HEPARIN REMARK 900 RELATED ID: 3IRI RELATED DB: PDB REMARK 900 RELATED ID: 3IRJ RELATED DB: PDB REMARK 900 RELATED ID: 3IRL RELATED DB: PDB HET SGN A 1 20 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 15 HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETNAM IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETSYN SGN N,O6-DISULFO-GLUCOSAMINE; 6-O-SULFO-N-SULFO-ALPHA-D- HETSYN 2 SGN GLUCOSAMINE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETSYN 3 SGN GLUCOSE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; HETSYN 4 SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-GLUCOSE HETSYN IDS O2-SULFO-GLUCURONIC ACID; 2-O-SULFO-ALPHA-L-IDURONIC HETSYN 2 IDS ACID; 2-O-SULFO-L-IDURONIC ACID; 2-O-SULFO-IDURONIC HETSYN 3 IDS ACID FORMUL 1 SGN 15(C6 H13 N O11 S2) FORMUL 1 IDS 15(C6 H10 O10 S) LINK O4 SGN A 1 C1 IDS A 2 1555 1555 1.40 LINK O4 IDS A 2 C1 SGN A 3 1555 1555 1.40 LINK O4 SGN A 3 C1 IDS A 4 1555 1555 1.40 LINK O4 IDS A 4 C1 SGN A 5 1555 1555 1.40 LINK O4 SGN A 5 C1 IDS A 6 1555 1555 1.40 LINK O4 IDS A 6 C1 SGN A 7 1555 1555 1.40 LINK O4 SGN A 7 C1 IDS A 8 1555 1555 1.40 LINK O4 IDS A 8 C1 SGN A 9 1555 1555 1.40 LINK O4 SGN A 9 C1 IDS A 10 1555 1555 1.40 LINK O4 IDS A 10 C1 SGN A 11 1555 1555 1.40 LINK O4 SGN A 11 C1 IDS A 12 1555 1555 1.40 LINK O4 IDS A 12 C1 SGN A 13 1555 1555 1.40 LINK O4 SGN A 13 C1 IDS A 14 1555 1555 1.40 LINK O4 IDS A 14 C1 SGN A 15 1555 1555 1.40 LINK O4 SGN A 15 C1 IDS A 16 1555 1555 1.40 LINK O4 IDS A 16 C1 SGN A 17 1555 1555 1.40 LINK O4 SGN A 17 C1 IDS A 18 1555 1555 1.40 LINK O4 IDS A 18 C1 SGN A 19 1555 1555 1.40 LINK O4 SGN A 19 C1 IDS A 20 1555 1555 1.40 LINK O4 IDS A 20 C1 SGN A 21 1555 1555 1.40 LINK O4 SGN A 21 C1 IDS A 22 1555 1555 1.40 LINK O4 IDS A 22 C1 SGN A 23 1555 1555 1.40 LINK O4 SGN A 23 C1 IDS A 24 1555 1555 1.40 LINK O4 IDS A 24 C1 SGN A 25 1555 1555 1.40 LINK O4 SGN A 25 C1 IDS A 26 1555 1555 1.40 LINK O4 IDS A 26 C1 SGN A 27 1555 1555 1.40 LINK O4 SGN A 27 C1 IDS A 28 1555 1555 1.40 LINK O4 IDS A 28 C1 SGN A 29 1555 1555 1.40 LINK O4 SGN A 29 C1 IDS A 30 1555 1555 1.40 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