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3E80
Biol. Unit 3
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, 8)
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
2
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
(8, 8)
Info
All Sites
1: CC2 (SOFTWARE)
2: CC3 (SOFTWARE)
3: CC4 (SOFTWARE)
4: CC5 (SOFTWARE)
5: CC6 (SOFTWARE)
6: CC7 (SOFTWARE)
7: CC8 (SOFTWARE)
8: CC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
CC2
SOFTWARE
HIS C:408 , ASP C:425 , HIS C:451 , HOH C:778 , HOH C:779
BINDING SITE FOR RESIDUE ZN C 3
2
CC3
SOFTWARE
LYS C:102 , THR C:105 , MAN C:774
BINDING SITE FOR RESIDUE RAM C 773
3
CC4
SOFTWARE
LEU C:104 , THR C:134 , RAM C:773 , GCU C:775 , HOH C:829
BINDING SITE FOR RESIDUE MAN C 774
4
CC5
SOFTWARE
THR C:134 , MAN C:774 , XYS C:776 , HOH C:829
BINDING SITE FOR RESIDUE GCU C 775
5
CC6
SOFTWARE
GCU C:775
BINDING SITE FOR RESIDUE XYS C 776
6
CC7
SOFTWARE
PO4 C:6 , ASP C:145 , ARG C:148 , GLY C:201 , HIS C:202 , GLU C:205 , TYR C:257 , ARG C:261 , ASN C:405 , HIS C:406 , TYR C:429 , TYR C:436 , ASN C:437 , GLY C:469 , GLY C:470 , HOH C:815 , HOH C:903 , HOH C:908 , HOH C:924
BINDING SITE FOR RESIDUE HS2 C 777
7
CC8
SOFTWARE
PRO C:611 , ASN C:615 , ASP C:665 , TYR C:666
BINDING SITE FOR RESIDUE PO4 C 4
8
CC9
SOFTWARE
PHE C:95 , ARG C:148 , TYR C:257 , HS2 C:777
BINDING SITE FOR RESIDUE PO4 C 6
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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
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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 C
Asymmetric Unit 1
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Show PDB file:
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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