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4IEF
Asym. Unit
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
(8, 29)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BA
4
Ligand/Ion
BARIUM ION
2
CA
14
Ligand/Ion
CALCIUM ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
CSD
4
Mod. Amino Acid
3-SULFINOALANINE
5
GOL
1
Ligand/Ion
GLYCEROL
6
MG
1
Ligand/Ion
MAGNESIUM ION
7
NA
3
Ligand/Ion
SODIUM ION
8
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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Sites
(25, 25)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:99 , GLN A:200
BINDING SITE FOR RESIDUE CL A 301
02
AC2
SOFTWARE
GLU B:390 , HIS B:395 , ASP B:521 , HOH B:916 , HOH B:917
BINDING SITE FOR RESIDUE BA B 701
03
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
04
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
05
AC5
SOFTWARE
ASP B:613 , GLU B:639 , HOH D:816 , HOH D:917
BINDING SITE FOR RESIDUE CA B 704
06
AC6
SOFTWARE
ASP B:614 , HOH B:813 , ASP D:614
BINDING SITE FOR RESIDUE CA B 705
07
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
08
AC8
SOFTWARE
GLU D:390 , HIS D:395 , ASP D:521
BINDING SITE FOR RESIDUE BA D 701
09
AC9
SOFTWARE
ASP D:307 , PHE D:478 , GLU D:487 , HOH D:832 , HOH D:833 , HOH D:898
BINDING SITE FOR RESIDUE CA D 702
10
BC1
SOFTWARE
ILE C:159 , VAL D:329 , ASP D:332 , TYR D:334 , GLU D:336 , HOH D:834
BINDING SITE FOR RESIDUE CA D 703
11
BC2
SOFTWARE
HOH B:815 , HOH B:947 , ASP D:613 , GLU D:639 , HOH D:899
BINDING SITE FOR RESIDUE CA D 704
12
BC3
SOFTWARE
GLU F:390 , HIS F:395 , ASP F:521 , HOH F:876 , HOH F:877
BINDING SITE FOR RESIDUE BA F 701
13
BC4
SOFTWARE
ILE E:159 , VAL F:329 , ASP F:332 , TYR F:334 , GLU F:336 , HOH F:817
BINDING SITE FOR RESIDUE CA F 702
14
BC5
SOFTWARE
ASP F:307 , PHE F:478 , GLU F:487 , HOH F:836 , HOH F:837
BINDING SITE FOR RESIDUE CA F 703
15
BC6
SOFTWARE
ASP F:613 , GLU F:639
BINDING SITE FOR RESIDUE CA F 704
16
BC7
SOFTWARE
ASP F:614 , ASP H:614
BINDING SITE FOR RESIDUE CA F 705
17
BC8
SOFTWARE
GLU F:254 , HOH F:810 , ASP H:258 , HOH H:911
BINDING SITE FOR RESIDUE NA F 706
18
BC9
SOFTWARE
ASP F:616 , HOH F:829 , HOH F:929 , ASP H:255 , HOH H:921 , HOH H:922
BINDING SITE FOR RESIDUE NA F 707
19
CC1
SOFTWARE
ASP F:258 , GLU H:254
BINDING SITE FOR RESIDUE NA F 708
20
CC2
SOFTWARE
GLU H:390 , HIS H:395 , ASP H:521 , HOH H:876 , HOH H:877
BINDING SITE FOR RESIDUE BA H 701
21
CC3
SOFTWARE
ILE G:159 , VAL H:329 , ASP H:332 , TYR H:334 , GLU H:336 , HOH H:825
BINDING SITE FOR RESIDUE CA H 702
22
CC4
SOFTWARE
ASP H:307 , PHE H:478 , GLU H:487 , GOL H:706 , HOH H:839
BINDING SITE FOR RESIDUE CA H 703
23
CC5
SOFTWARE
ASP H:613 , GLU H:639
BINDING SITE FOR RESIDUE CA H 704
24
CC6
SOFTWARE
ASP F:614 , HOH F:810 , HOH F:929 , GLU H:254 , ASP H:258
BINDING SITE FOR RESIDUE MG H 705
25
CC7
SOFTWARE
ASP H:307 , GLU H:345 , PHE H:478 , TYR H:480 , ASN H:481 , VAL H:482 , PRO H:483 , CA H:703 , HOH H:839
BINDING SITE FOR RESIDUE GOL H 706
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
(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)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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]
Atom Selection
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Protein & NOT Site
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Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
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