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1W3Y
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF S. PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH PALMITOYL-VITAMIN C
Authors
:
D. J. Rigden, M. J. Jedrzejas
Date
:
21 Jul 04 (Deposition) - 26 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
(Alfa5/Alfa5) Barrel, Lyase, Peptidoglycan-Anchor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Botzki, D. J. Rigden, S. Braun, M. Nukui, S. Salmen, J. Hoechstetter, G. Bernhardt, S. Dove, M. J. Jedrzejas, A. Buschauer
L-Ascorbic Acid 6-Hexadecanoate, A Potent Hyaluronidase Inhibitor: X-Ray Structure And Molecular Modeling Of Enzyme-Inhibitor Complexes
J. Biol. Chem. V. 279 45990 2004
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: (2E,4R,5S)-2,3,4,5-TETRAHYDROXY-6-... (PVCa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
3a: D-XYLITOL (XYLa)
3b: D-XYLITOL (XYLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PVC
1
Ligand/Ion
(2E,4R,5S)-2,3,4,5-TETRAHYDROXY-6-(PALMITOYLOXY)HEX-2-ENOIC ACID
2
SO4
5
Ligand/Ion
SULFATE ION
3
XYL
2
Ligand/Ion
D-XYLITOL
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:401 , LYS A:560 , LEU A:574 , VAL A:635 , ASP A:675 , LYS A:831 , HOH A:2311 , HOH A:2408 , HOH A:2555 , HOH A:2556
BINDING SITE FOR RESIDUE XYL A1892
2
AC2
SOFTWARE
TYR A:391 , THR A:400 , ASN A:401 , LYS A:549 , ARG A:572 , THR A:573 , GLN A:878 , HOH A:2301 , HOH A:2495 , HOH A:2496 , HOH A:2498 , HOH A:2557
BINDING SITE FOR RESIDUE XYL A1893
3
AC3
SOFTWARE
HIS A:578 , LYS A:581 , LYS A:584 , SER A:630 , HOH A:2558 , HOH A:2559
BINDING SITE FOR RESIDUE SO4 A1895
4
AC4
SOFTWARE
ALA A:628 , ASP A:629 , SER A:630 , HOH A:2377 , HOH A:2560
BINDING SITE FOR RESIDUE SO4 A1896
5
AC5
SOFTWARE
GLN A:729 , LYS A:748 , LYS A:749 , HOH A:2454
BINDING SITE FOR RESIDUE SO4 A1897
6
AC6
SOFTWARE
HIS A:334 , LYS A:811 , HOH A:2561 , HOH A:2562
BINDING SITE FOR RESIDUE SO4 A1898
7
AC7
SOFTWARE
ARG A:267 , LYS A:444 , LYS A:645 , HOH A:2563 , HOH A:2564
BINDING SITE FOR RESIDUE SO4 A1899
8
AC8
SOFTWARE
ASN A:290 , TRP A:291 , TRP A:292 , ARG A:336 , GLU A:388 , HIS A:399 , THR A:400 , TYR A:408 , ARG A:462 , ARG A:466 , MET A:579 , ASN A:580 , HOH A:2185 , HOH A:2553 , HOH A:2554
BINDING SITE FOR RESIDUE PVC A1891
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
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_d1w3ya1 (A:170-540)
2a: SCOP_d1w3ya2 (A:815-890)
3a: SCOP_d1w3ya3 (A:541-814)
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Families
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)
Protein Domains
(
)
(
)
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
d1w3ya1
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
d1w3ya2
A:815-890
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
d1w3ya3
A:541-814
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1w3yA02 (A:170-542)
2a: CATH_1w3yA01 (A:548-804)
3a: CATH_1w3yA03 (A:805-890)
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)
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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
1w3yA02
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
1w3yA01
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
1w3yA03
A:805-890
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Lyase_8_1w3yA01 (A:537-807)
2a: PFAM_Lyase_8_N_1w3yA02 (A:181-503)
3a: PFAM_Lyase_8_C_1w3yA03 (A:815-887)
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(
)
Organisms
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)
(
)
Clan
:
Gal_mutarotase
(81)
Family
:
Lyase_8
(15)
Streptococcus pneumoniae
(11)
1a
Lyase_8-1w3yA01
A:537-807
Clan
:
Hy-ly_N
(15)
Family
:
Lyase_8_N
(15)
Streptococcus pneumoniae
(11)
2a
Lyase_8_N-1w3yA02
A:181-503
Clan
:
no clan defined [family: Lyase_8_C]
(15)
Family
:
Lyase_8_C
(15)
Streptococcus pneumoniae
(11)
3a
Lyase_8_C-1w3yA03
A:815-887
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Chain A
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (136 KB)
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