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1OJM
Asym. Unit
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Asym.Unit (137 KB)
Biol.Unit 1 (132 KB)
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(1)
Title
:
SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN DISACCHARIDE
Authors
:
D. J. Rigden, M. J. Jedrzejas
Date
:
11 Jul 03 (Deposition) - 30 Oct 03 (Release) - 23 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Lyase, Protein-Carbohydrate Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. J. Rigden, M. J. Jedrzejas
Structures Of Streptococcus Pneumoniae Hyaluronate Lyase In Complex With Chondroitin And Chondroitin Sulfate Disaccharides: Insights Into Specificity And Mechanism Of Action
J. Biol. Chem. V. 278 50596 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: 4,5-DEHYDRO-D-GLUCURONIC ACID (GCDa)
2a: N-ACETYL-D-GALACTOSAMINE (NGAa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
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No.
Name
Count
Type
Full Name
1
GCD
1
Ligand/Ion
4,5-DEHYDRO-D-GLUCURONIC ACID
2
NGA
1
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
3
SO4
4
Ligand/Ion
SULFATE ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:578 , LYS A:581 , LYS A:584 , SER A:630 , HOH A:2352 , HOH A:2570
BINDING SITE FOR RESIDUE SO4 A1200
2
AC2
SOFTWARE
ALA A:628 , ASP A:629 , SER A:630 , HOH A:2571
BINDING SITE FOR RESIDUE SO4 A1201
3
AC3
SOFTWARE
LYS A:748 , LYS A:749
BINDING SITE FOR RESIDUE SO4 A1202
4
AC4
SOFTWARE
HIS A:334 , LYS A:344 , LYS A:811
BINDING SITE FOR RESIDUE SO4 A1203
5
AC5
SOFTWARE
ARG A:243 , TRP A:292 , ARG A:300 , ALA A:407 , TYR A:408 , ARG A:462 , ARG A:466 , GLU A:477 , HOH A:2109 , HOH A:2169 , HOH A:2251 , HOH A:2562 , HOH A:2563 , HOH A:2564 , HOH A:2565 , HOH A:2566 , HOH A:2567 , HOH A:2568 , HOH A:2569
BINDING SITE FOR RESIDUES GCD A 900 AND NGA A 901
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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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.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1ojma1 (A:170-540)
2a: SCOP_d1ojma2 (A:815-891)
3a: SCOP_d1ojma3 (A:541-814)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Chondroitin AC/alginate lyase
(45)
Family
:
Hyaluronate lyase-like catalytic, N-terminal domain
(40)
Protein domain
:
Hyaluronate lyase
(21)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(18)
1a
d1ojma1
A:170-540
Class
:
All beta proteins
(24004)
Fold
:
Hyaluronate lyase-like, C-terminal domain
(40)
Superfamily
:
Hyaluronate lyase-like, C-terminal domain
(40)
Family
:
Hyaluronate lyase-like, C-terminal domain
(35)
Protein domain
:
Hyaluronate lyase
(21)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(18)
2a
d1ojma2
A:815-891
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
Hyaluronate lyase-like, central domain
(35)
Protein domain
:
Hyaluronate lyase
(21)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(18)
3a
d1ojma3
A:541-814
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1ojmA02 (A:170-542)
2a: CATH_1ojmA01 (A:548-804)
3a: CATH_1ojmA03 (A:805-890)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha/alpha barrel
(251)
Topology
:
Glycosyltransferase
(233)
Homologous Superfamily
:
[code=1.50.10.100, no name defined]
(43)
Streptococcus pneumoniae. Organism_taxid: 1313.
(17)
1a
1ojmA02
A:170-542
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Streptococcus pneumoniae. Organism_taxid: 1313.
(17)
2a
1ojmA01
A:548-804
Architecture
:
Sandwich
(5577)
Topology
:
Chondroitinase Ac; Chain A, domain 3
(40)
Homologous Superfamily
:
Chondroitinase Ac; Chain A, domain 3
(40)
Streptococcus pneumoniae. Organism_taxid: 1313.
(17)
3a
1ojmA03
A:805-890
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Asym.Unit (137 KB)
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