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1WCQ
Asym. Unit
Info
Asym.Unit (305 KB)
Biol.Unit 1 (102 KB)
Biol.Unit 2 (104 KB)
Biol.Unit 3 (101 KB)
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(1)
Title
:
MUTAGENESIS OF THE NUCLEOPHILIC TYROSINE IN A BACTERIAL SIALIDASE TO PHENYLALANINE.
Authors
:
S. Newstead, J. N. Watson, A. J. Bennet, G. Taylor
Date
:
19 Nov 04 (Deposition) - 12 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Hydrolase, Sialidase, Micromonospora Viridifaciens, Hydrolase Neuraminidase, Glycosidase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
J. N. Watson, S. Newstead, A. A. Narine, G. Taylor, A. J. Bennet
Two Nucleophilic Mutants Of The Micromonospora Viridifaciens Sialidase Operate With Retention Of Configuration By Two Different Mechanisms.
Chembiochem V. 6 1439 2005
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURA... (DANa)
1b: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURA... (DANb)
1c: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURA... (DANc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAN
3
Ligand/Ion
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2
GOL
7
Ligand/Ion
GLYCEROL
3
NA
3
Ligand/Ion
SODIUM ION
[
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Sites
(13, 13)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:528 , ASP A:531 , ASN A:533 , THR A:536 , ALA A:639 , GLU A:640
BINDING SITE FOR RESIDUE NA A1648
02
AC2
SOFTWARE
ASN B:528 , ASP B:531 , ASN B:533 , THR B:536 , ALA B:639 , GLU B:640
BINDING SITE FOR RESIDUE NA B1648
03
AC3
SOFTWARE
ASN C:528 , ASP C:531 , ASN C:533 , THR C:536 , ALA C:639 , GLU C:640
BINDING SITE FOR RESIDUE NA C1648
04
AC4
SOFTWARE
ARG A:68 , ILE A:69 , ARG A:87 , ASP A:92 , ASP A:131 , PHE A:203 , ASP A:259 , ARG A:276 , ARG A:342 , PHE A:370 , HOH A:2024 , HOH A:2025 , HOH A:2318 , HOH A:2320
BINDING SITE FOR RESIDUE DAN A1651
05
AC5
SOFTWARE
ARG B:68 , ILE B:69 , ARG B:87 , ASP B:92 , ASP B:131 , PHE B:203 , ASP B:259 , GLU B:260 , ARG B:276 , ARG B:342 , PHE B:370 , HOH B:2082 , HOH B:2397 , HOH B:2398 , HOH B:2399
BINDING SITE FOR RESIDUE DAN B1652
06
AC6
SOFTWARE
ARG C:68 , ILE C:69 , ARG C:87 , ASP C:92 , ASP C:131 , PHE C:203 , PHE C:234 , ASP C:259 , GLU C:260 , ARG C:276 , ARG C:342 , PHE C:370 , HOH C:2044 , HOH C:2358 , HOH C:2359
BINDING SITE FOR RESIDUE DAN C1651
07
AC7
SOFTWARE
HIS A:633 , LYS A:634
BINDING SITE FOR RESIDUE GOL A1649
08
AC8
SOFTWARE
ARG A:571 , THR A:605 , LEU A:607 , HOH A:2316 , HOH A:2317
BINDING SITE FOR RESIDUE GOL A1650
09
AC9
SOFTWARE
PHE B:363 , PRO B:365 , TRP B:400 , SER B:439
BINDING SITE FOR RESIDUE GOL B1649
10
BC1
SOFTWARE
GLU B:522 , HIS B:539 , TRP B:542 , ARG B:572 , HOH B:2367
BINDING SITE FOR RESIDUE GOL B1650
11
BC2
SOFTWARE
ARG B:617 , HOH B:2395 , HOH B:2396 , ARG C:61 , GLN C:364
BINDING SITE FOR RESIDUE GOL B1651
12
BC3
SOFTWARE
VAL C:116 , VAL C:117 , SER C:118 , ALA C:119 , HIS C:186
BINDING SITE FOR RESIDUE GOL C1649
13
BC4
SOFTWARE
GLU C:522 , HIS C:539 , TRP C:542 , ARG C:572 , GLU C:578
BINDING SITE FOR RESIDUE GOL C1650
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:496-646,B:496-646,C:496-646)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
NANH_MICVI
496-646
3
A:496-646
B:496-646
C:496-646
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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, 9)
Info
All SCOP Domains
1a: SCOP_d1wcqa3 (A:47-402)
1b: SCOP_d1wcqb3 (B:47-402)
1c: SCOP_d1wcqc3 (C:49-402)
2a: SCOP_d1wcqa2 (A:506-647)
2b: SCOP_d1wcqb2 (B:506-647)
2c: SCOP_d1wcqc2 (C:506-647)
3a: SCOP_d1wcqa1 (A:403-505)
3b: SCOP_d1wcqb1 (B:403-505)
3c: SCOP_d1wcqc1 (C:403-505)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
Sialidases
(238)
Family
:
Sialidases (neuraminidases)
(178)
Protein domain
:
automated matches
(38)
Micromonospora viridifaciens [TaxId: 1881]
(3)
1a
d1wcqa3
A:47-402
1b
d1wcqb3
B:47-402
1c
d1wcqc3
C:49-402
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Micromonospora viridifaciens [TaxId: 1881]
(3)
2a
d1wcqa2
A:506-647
2b
d1wcqb2
B:506-647
2c
d1wcqc2
C:506-647
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
automated matches
(93)
Protein domain
:
automated matches
(93)
Micromonospora viridifaciens [TaxId: 1881]
(3)
3a
d1wcqa1
A:403-505
3b
d1wcqb1
B:403-505
3c
d1wcqc1
C:403-505
[
close SCOP info
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CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_1wcqA01 (A:47-400)
1b: CATH_1wcqB01 (B:47-400)
1c: CATH_1wcqC01 (C:49-400)
2a: CATH_1wcqA02 (A:401-502)
2b: CATH_1wcqB02 (B:401-502)
2c: CATH_1wcqC02 (C:401-502)
3a: CATH_1wcqA03 (A:503-647)
3b: CATH_1wcqB03 (B:503-647)
3c: CATH_1wcqC03 (C:503-647)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
[code=2.120.10.10, no name defined]
(150)
Micromonospora viridifaciens. Organism_taxid: 1881.
(9)
1a
1wcqA01
A:47-400
1b
1wcqB01
B:47-400
1c
1wcqC01
C:49-400
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Micromonospora viridifaciens. Organism_taxid: 1881.
(7)
2a
1wcqA02
A:401-502
2b
1wcqB02
B:401-502
2c
1wcqC02
C:401-502
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Micromonospora viridifaciens. Organism_taxid: 1881.
(7)
3a
1wcqA03
A:503-647
3b
1wcqB03
B:503-647
3c
1wcqC03
C:503-647
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_NPCBM_assoc_1wcqC01 (C:415-489)
1b: PFAM_NPCBM_assoc_1wcqC02 (C:415-489)
1c: PFAM_NPCBM_assoc_1wcqC03 (C:415-489)
2a: PFAM_F5_F8_type_C_1wcqC04 (C:512-641)
2b: PFAM_F5_F8_type_C_1wcqC05 (C:512-641)
2c: PFAM_F5_F8_type_C_1wcqC06 (C:512-641)
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Clans
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Organisms
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)
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)
Clan
:
E-set
(290)
Family
:
NPCBM_assoc
(3)
Micromonospora viridifaciens
(3)
1a
NPCBM_assoc-1wcqC01
C:415-489
1b
NPCBM_assoc-1wcqC02
C:415-489
1c
NPCBM_assoc-1wcqC03
C:415-489
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Micromonospora viridifaciens
(3)
2a
F5_F8_type_C-1wcqC04
C:512-641
2b
F5_F8_type_C-1wcqC05
C:512-641
2c
F5_F8_type_C-1wcqC06
C:512-641
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