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2BZD
Asym. Unit
Info
Asym.Unit (311 KB)
Biol.Unit 1 (102 KB)
Biol.Unit 2 (105 KB)
Biol.Unit 3 (107 KB)
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(1)
Title
:
GALACTOSE RECOGNITION BY THE CARBOHYDRATE-BINDING MODULE OF A BACTERIAL SIALIDASE.
Authors
:
S. L. Newstead, G. Taylor
Date
:
16 Aug 05 (Deposition) - 19 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Sialidase, Hydrolase, Carbohydrate Binding Module, Glycosidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. L. Newstead, J. N. Watson, A. J. Bennet, G. Taylor
Galactose Recognition By The Carbohydrate-Binding Module Of A Bacterial Sialidase.
Acta Crystallogr. , Sect. D V. 61 1483 2005
[
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
2
GOL
3
Ligand/Ion
GLYCEROL
3
NA
3
Ligand/Ion
SODIUM ION
[
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Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:522 , HIS A:539 , TRP A:542 , ARG A:572 , GLU A:578 , TYR A:635 , HOH A:2358 , HOH A:2359
BINDING SITE FOR RESIDUE GAL A1649
2
AC2
SOFTWARE
GLU B:522 , HIS B:539 , TRP B:542 , ARG B:572 , TYR B:635 , HOH B:2487 , HOH B:2488 , HOH C:2635
BINDING SITE FOR RESIDUE GAL B1649
3
AC3
SOFTWARE
GLU C:522 , HIS C:539 , TRP C:542 , ARG C:572 , TYR C:635 , HOH C:2645
BINDING SITE FOR RESIDUE GAL C1649
4
AC4
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
5
AC5
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
6
AC6
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
7
AC7
SOFTWARE
ARG A:68 , ARG A:276 , ARG A:342 , TYR A:370 , HOH A:2360 , HOH A:2361
BINDING SITE FOR RESIDUE GOL A1650
8
AC8
SOFTWARE
ARG B:68 , ARG B:276 , ARG B:342 , TYR B:370
BINDING SITE FOR RESIDUE GOL B1650
9
AC9
SOFTWARE
ARG C:68 , ASP C:92 , ARG C:276 , ARG C:342 , TYR C:370 , HOH C:2356 , HOH C:2646
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_d2bzda1 (A:47-402)
1b: SCOP_d2bzdb1 (B:47-402)
1c: SCOP_d2bzdc1 (C:48-402)
2a: SCOP_d2bzda3 (A:506-647)
2b: SCOP_d2bzdb3 (B:506-647)
2c: SCOP_d2bzdc3 (C:506-647)
3a: SCOP_d2bzda2 (A:403-505)
3b: SCOP_d2bzdb2 (B:403-505)
3c: SCOP_d2bzdc2 (C:403-505)
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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
d2bzda1
A:47-402
1b
d2bzdb1
B:47-402
1c
d2bzdc1
C:48-402
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
d2bzda3
A:506-647
2b
d2bzdb3
B:506-647
2c
d2bzdc3
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
d2bzda2
A:403-505
3b
d2bzdb2
B:403-505
3c
d2bzdc2
C:403-505
[
close SCOP info
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CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_2bzdA01 (A:47-400)
1b: CATH_2bzdB01 (B:47-400)
1c: CATH_2bzdC01 (C:48-400)
2a: CATH_2bzdA02 (A:401-502)
2b: CATH_2bzdB02 (B:401-502)
2c: CATH_2bzdC02 (C:401-502)
3a: CATH_2bzdA03 (A:503-647)
3b: CATH_2bzdB03 (B:503-647)
3c: CATH_2bzdC03 (C:503-647)
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)
Homologous Superfamilies
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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
2bzdA01
A:47-400
1b
2bzdB01
B:47-400
1c
2bzdC01
C:48-400
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Micromonospora viridifaciens. Organism_taxid: 1881.
(7)
2a
2bzdA02
A:401-502
2b
2bzdB02
B:401-502
2c
2bzdC02
C:401-502
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Micromonospora viridifaciens. Organism_taxid: 1881.
(7)
3a
2bzdA03
A:503-647
3b
2bzdB03
B:503-647
3c
2bzdC03
C:503-647
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (311 KB)
Header - Asym.Unit
Biol.Unit 1 (102 KB)
Header - Biol.Unit 1
Biol.Unit 2 (105 KB)
Header - Biol.Unit 2
Biol.Unit 3 (107 KB)
Header - Biol.Unit 3
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