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2V5C
Biol. Unit 1
Info
Asym.Unit (218 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (108 KB)
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(1)
Title
:
FAMILY 84 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS, 2.1 ANGSTROM STRUCTURE
Authors
:
E. Ficko-Blean, K. J. Gregg, J. J. Adams, J. H. Hehemann, S. J. Smith, M. Czjzek, A. B. Boraston
Date
:
02 Oct 08 (Deposition) - 27 Jan 09 (Release) - 14 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Glycosidase, Clostridium Perfringens, Gh84, Gh84C, Hydrolase, Coiled Coil, Family 84 Glycoside Hydrolase, Carbohydrate Binding Module
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Reference
:
E. Ficko-Blean, K. J. Gregg, J. J. Adams, J. H. Hehemann, S. J. Smith, M. Czjzek, A. B. Boraston
Portrait Of An Enzyme: A Complete Structural Analysis Of A Multi-Modular Beta-N- Acetylglucosaminidase From Clostridium Perfringens
J. Biol. Chem. V. 284 9876 2009
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Hetero Components
(1, 3)
Info
All Hetero Components
2a: CACODYLATE ION (CACa)
2b: CACODYLATE ION (CACb)
2c: CACODYLATE ION (CACc)
2d: CACODYLATE ION (CACd)
2e: CACODYLATE ION (CACe)
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
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No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CAC
3
Ligand/Ion
CACODYLATE ION
3
NA
-1
Ligand/Ion
SODIUM ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:557 , ALA A:597 , LEU A:598 , SER A:600 , ALA A:602 , HOH A:2603 , HOH A:2611
BINDING SITE FOR RESIDUE CA A1625
2
AC2
SOFTWARE
GLU A:73 , GLU A:108 , ASP A:111 , HOH A:2079
BINDING SITE FOR RESIDUE CA A1626
3
AC3
SOFTWARE
HIS A:413 , TYR A:456 , HOH A:2624
BINDING SITE FOR RESIDUE CAC A1627
4
AC4
SOFTWARE
GLY A:187 , VAL A:371 , ASN A:396 , ASP A:401 , ASN A:429 , LEU B:623
BINDING SITE FOR RESIDUE CAC A1628
5
AC5
SOFTWARE
TYR A:583 , LYS A:587 , LEU A:617 , ASP A:620 , HOH A:2626
BINDING SITE FOR RESIDUE CAC A1629
6
AC6
SOFTWARE
MET A:571 , TYR A:583 , ALA A:616 , LEU A:617 , PHE A:619 , HOH A:2571
BINDING SITE FOR RESIDUE NA A1630
7
BC1
SOFTWARE
LEU A:623 , GLY B:187 , VAL B:370 , VAL B:371 , ASN B:396 , VAL B:399 , ASP B:401 , ASN B:429 , HOH B:2265
BINDING SITE FOR RESIDUE CAC B1628
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2v5ca3 (A:496-624)
1b: SCOP_d2v5cb3 (B:496-624)
2a: SCOP_d2v5ca1 (A:41-178)
2b: SCOP_d2v5cb1 (B:41-178)
3a: SCOP_d2v5ca2 (A:179-495)
3b: SCOP_d2v5cb2 (B:179-495)
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Protein Domains
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Hyaluronidase domain-like
(25)
Superfamily
:
Hyaluronidase post-catalytic domain-like
(20)
Family
:
Hyaluronidase post-catalytic domain-like
(15)
Protein domain
:
Hyaluronidase, post-catalytic domain 3
(7)
Clostridium perfringens [TaxId: 1502]
(7)
1a
d2v5ca3
A:496-624
1b
d2v5cb3
B:496-624
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
beta-N-acetylhexosaminidase-like domain
(54)
Family
:
Hyaluronidase N-terminal domain-like
(15)
Protein domain
:
Hyaluronidase N-terminal domain
(7)
Clostridium perfringens [TaxId: 1502]
(7)
2a
d2v5ca1
A:41-178
2b
d2v5cb1
B:41-178
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
alpha-D-glucuronidase/Hyaluronidase catalytic domain
(32)
Protein domain
:
Hyaluronidase catalytic domain
(7)
Clostridium perfringens [TaxId: 1502]
(7)
3a
d2v5ca2
A:179-495
3b
d2v5cb2
B:179-495
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CATH Domains
(0, 0)
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_NAGidase_2v5cB01 (B:182-482)
1b: PFAM_NAGidase_2v5cB02 (B:182-482)
2a: PFAM_Glyco_hydro_20b_2v5cB03 (B:118-177)
2b: PFAM_Glyco_hydro_20b_2v5cB04 (B:118-177)
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Clan
:
Glyco_hydro_tim
(488)
Family
:
NAGidase
(15)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(5)
1a
NAGidase-2v5cB01
B:182-482
1b
NAGidase-2v5cB02
B:182-482
Clan
:
no clan defined [family: Glyco_hydro_20b]
(22)
Family
:
Glyco_hydro_20b
(22)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(5)
2a
Glyco_hydro_20b-2v5cB03
B:118-177
2b
Glyco_hydro_20b-2v5cB04
B:118-177
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Chain A
Asymmetric Unit 1
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Asym.Unit (218 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 KB)
Header - Biol.Unit 2
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