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4IEF
Biol. Unit 1
Info
Asym.Unit (826 KB)
Biol.Unit 1 (210 KB)
Biol.Unit 2 (210 KB)
Biol.Unit 3 (211 KB)
Biol.Unit 4 (209 KB)
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(1)
Title
:
COMPLEX OF PORPHYROMONAS GINGIVALIS RGPB PRO- AND MATURE DOMAINS
Authors
:
I. De Diego, F. T. Veillard, T. Guevara, B. Potempa, M. Sztukowska, J. P F. X. Gomis-Ruth
Date
:
13 Dec 12 (Deposition) - 10 Apr 13 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Alpha/Beta/Alpha Sandwich, Cysteine Endopeptidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. De Diego, F. T. Veillard, T. Guevara, B. Potempa, M. Sztukowska, J. Potempa, F. X. Gomis-Ruth
Porphyromonas Gingivalis Virulence Factor Gingipain Rgpb Shows A Unique Zymogenic Mechanism For Cysteine Peptidases.
J. Biol. Chem. V. 288 14287 2013
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: BARIUM ION (BAa)
1b: BARIUM ION (BAb)
1c: BARIUM ION (BAc)
1d: BARIUM ION (BAd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
2m: CALCIUM ION (CAm)
2n: CALCIUM ION (CAn)
3a: CHLORIDE ION (CLa)
4a: 3-SULFINOALANINE (CSDa)
4b: 3-SULFINOALANINE (CSDb)
4c: 3-SULFINOALANINE (CSDc)
4d: 3-SULFINOALANINE (CSDd)
5a: GLYCEROL (GOLa)
6a: MAGNESIUM ION (MGa)
7a: SODIUM ION (NAa)
7b: SODIUM ION (NAb)
7c: SODIUM ION (NAc)
8a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
BA
-1
Ligand/Ion
BARIUM ION
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
CSD
1
Mod. Amino Acid
3-SULFINOALANINE
5
GOL
-1
Ligand/Ion
GLYCEROL
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
NA
-1
Ligand/Ion
SODIUM ION
8
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
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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: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:99 , GLN A:200
BINDING SITE FOR RESIDUE CL A 301
2
AC2
SOFTWARE
GLU B:390 , HIS B:395 , ASP B:521 , HOH B:916 , HOH B:917
BINDING SITE FOR RESIDUE BA B 701
3
AC3
SOFTWARE
ILE A:159 , VAL B:329 , ASP B:332 , TYR B:334 , GLU B:336 , HOH B:831
BINDING SITE FOR RESIDUE CA B 702
4
AC4
SOFTWARE
ASP B:307 , PHE B:478 , GLU B:487 , HOH B:845 , HOH B:846 , HOH B:847
BINDING SITE FOR RESIDUE CA B 703
5
AC5
SOFTWARE
ASP B:613 , GLU B:639 , HOH D:816 , HOH D:917
BINDING SITE FOR RESIDUE CA B 704
6
AC6
SOFTWARE
ASP B:614 , HOH B:813 , ASP D:614
BINDING SITE FOR RESIDUE CA B 705
7
AC7
SOFTWARE
GLU B:254 , ASP B:258 , ASP B:614 , HOH B:949 , GLU D:254 , ASP D:258 , ASP D:614 , HOH D:914
BINDING SITE FOR RESIDUE TRS B 706
8
BC2
SOFTWARE
HOH B:815 , HOH B:947 , ASP D:613 , GLU D:639 , HOH D:899
BINDING SITE FOR RESIDUE CA D 704
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4iefb2 (B:580-661)
1b: SCOP_d4iefd2 (D:580-661)
1c: SCOP_d4ieff2 (F:580-661)
1d: SCOP_d4iefh2 (H:580-661)
2a: SCOP_d4iefb1 (B:239-579)
2b: SCOP_d4iefd1 (D:238-579)
2c: SCOP_d4ieff1 (F:238-579)
2d: SCOP_d4iefh1 (H:238-579)
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Classes
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
automated matches
(93)
Protein domain
:
automated matches
(93)
Porphyromonas gingivalis [TaxId: 242619]
(1)
1a
d4iefb2
B:580-661
1b
d4iefd2
D:580-661
1c
d4ieff2
F:580-661
1d
d4iefh2
H:580-661
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Caspase-like
(92)
Superfamily
:
Caspase-like
(92)
Family
:
Gingipain R (RgpB), N-terminal domain
(2)
Protein domain
:
automated matches
(1)
Porphyromonas gingivalis [TaxId: 242619]
(1)
2a
d4iefb1
B:239-579
2b
d4iefd1
D:238-579
2c
d4ieff1
F:238-579
2d
d4iefh1
H:238-579
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (826 KB)
Header - Asym.Unit
Biol.Unit 1 (210 KB)
Header - Biol.Unit 1
Biol.Unit 2 (210 KB)
Header - Biol.Unit 2
Biol.Unit 3 (211 KB)
Header - Biol.Unit 3
Biol.Unit 4 (209 KB)
Header - Biol.Unit 4
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