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3E80
Biol. Unit 1
Info
Asym.Unit (379 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (128 KB)
Biol.Unit 3 (128 KB)
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(1)
Title
:
STRUCTURE OF HEPARINASE II COMPLEXED WITH HEPARAN SULFATE DEGRADATION DISACCHARIDE PRODUCT
Authors
:
D. Shaya, M. Cygler
Date
:
19 Aug 08 (Deposition) - 30 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Alpha And Beta Lyase Fold, Alpha6/Alpha6 Incomplete Toroid, Sugar Binding Protein, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Shaya, W. Zhao, M. L. Garron, Z. Xiao, Q. Cui, Z. Zhang, T. Sulea, R. J. Linhardt, M. Cygler
Catalytic Mechanism Of Heparinase Ii Investigated By Site-Directed Mutagenesis And The Crystal Structure With It Substrate.
J. Biol. Chem. V. 285 20051 2010
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Hetero Components
(7, 10)
Info
All Hetero Components
1a: D-GLUCURONIC ACID (GCUa)
1b: D-GLUCURONIC ACID (GCUb)
1c: D-GLUCURONIC ACID (GCUc)
2a: 2-DEOXY-4-O-(4-DEOXY-ALPHA-L-THREO... (HS2a)
2b: 2-DEOXY-4-O-(4-DEOXY-ALPHA-L-THREO... (HS2b)
2c: 2-DEOXY-4-O-(4-DEOXY-ALPHA-L-THREO... (HS2c)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
4a: PYROGLUTAMIC ACID (PCAa)
4b: PYROGLUTAMIC ACID (PCAb)
4c: PYROGLUTAMIC ACID (PCAc)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
5e: PHOSPHATE ION (PO4e)
5f: PHOSPHATE ION (PO4f)
5g: PHOSPHATE ION (PO4g)
5h: PHOSPHATE ION (PO4h)
5i: PHOSPHATE ION (PO4i)
6a: ALPHA-L-RHAMNOSE (RAMa)
6b: ALPHA-L-RHAMNOSE (RAMb)
6c: ALPHA-L-RHAMNOSE (RAMc)
7a: XYLOPYRANOSE (XYSa)
7b: XYLOPYRANOSE (XYSb)
7c: XYLOPYRANOSE (XYSc)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
8c: ZINC ION (ZNc)
View:
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No.
Name
Count
Type
Full Name
1
GCU
1
Ligand/Ion
D-GLUCURONIC ACID
2
HS2
1
Ligand/Ion
2-DEOXY-4-O-(4-DEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANURONOSYL)-2-{[(1R)-1-HYDROXYETHYL]AMINO}-ALPHA-D-GLUCOPYRANOSE
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
PCA
1
Mod. Amino Acid
PYROGLUTAMIC ACID
5
PO4
4
Ligand/Ion
PHOSPHATE ION
6
RAM
1
Ligand/Ion
ALPHA-L-RHAMNOSE
7
XYS
1
Ligand/Ion
XYLOPYRANOSE
8
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:408 , ASP A:425 , HIS A:451 , HOH A:778 , HOH A:779 , HOH A:983
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
LYS A:102 , LEU A:104 , THR A:105 , MAN A:774 , HOH A:899
BINDING SITE FOR RESIDUE RAM A 773
03
AC3
SOFTWARE
THR A:134 , RAM A:773 , GCU A:775
BINDING SITE FOR RESIDUE MAN A 774
04
AC4
SOFTWARE
THR A:134 , MAN A:774 , XYS A:776 , HOH A:890
BINDING SITE FOR RESIDUE GCU A 775
05
AC5
SOFTWARE
GCU A:775
BINDING SITE FOR RESIDUE XYS A 776
06
AC6
SOFTWARE
PO4 A:2 , ASP A:145 , ARG A:148 , GLY A:201 , HIS A:202 , GLU A:205 , TYR A:257 , ARG A:261 , ASN A:405 , HIS A:406 , TYR A:429 , TYR A:436 , ASN A:437 , GLY A:469 , GLY A:470 , HOH A:832 , HOH A:939 , HOH A:973
BINDING SITE FOR RESIDUE HS2 A 777
07
AC7
SOFTWARE
PHE A:95 , ARG A:96 , ASP A:145 , ARG A:148 , TYR A:257 , HS2 A:777 , HOH A:928
BINDING SITE FOR RESIDUE PO4 A 2
08
AC8
SOFTWARE
GLY A:435 , TYR A:436 , ASN A:437
BINDING SITE FOR RESIDUE PO4 A 3
09
AC9
SOFTWARE
HIS A:682 , GLU A:683 , ALA A:698
BINDING SITE FOR RESIDUE PO4 A 5
10
BC1
SOFTWARE
PRO A:611 , ASN A:615 , ASP A:665 , TYR A:666 , HOH A:859
BINDING SITE FOR RESIDUE PO4 A 9
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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CATH Domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (379 KB)
Header - Asym.Unit
Biol.Unit 1 (129 KB)
Header - Biol.Unit 1
Biol.Unit 2 (128 KB)
Header - Biol.Unit 2
Biol.Unit 3 (128 KB)
Header - Biol.Unit 3
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