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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4IEF

Complex of Porphyromonas gingivalis RgpB pro- and mature domains

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004197	molecular_function	cysteine-type endopeptidase activity
B	0006508	biological_process	proteolysis
B	0008233	molecular_function	peptidase activity
B	0008234	molecular_function	cysteine-type peptidase activity
C	0004197	molecular_function	cysteine-type endopeptidase activity
D	0006508	biological_process	proteolysis
D	0008233	molecular_function	peptidase activity
D	0008234	molecular_function	cysteine-type peptidase activity
E	0004197	molecular_function	cysteine-type endopeptidase activity
F	0006508	biological_process	proteolysis
F	0008233	molecular_function	peptidase activity
F	0008234	molecular_function	cysteine-type peptidase activity
G	0004197	molecular_function	cysteine-type endopeptidase activity
H	0006508	biological_process	proteolysis
H	0008233	molecular_function	peptidase activity
H	0008234	molecular_function	cysteine-type peptidase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 301

Chain	Residue
A	ALA99
A	GLN200

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BA B 701

Chain	Residue
B	GLU390
B	HIS395
B	ASP521
B	HOH916
B	HOH917

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 702

Chain	Residue
B	ASP332
B	TYR334
B	GLU336
B	HOH831
A	ILE159
B	VAL329

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 703

Chain	Residue
B	ASP307
B	PHE478
B	GLU487
B	HOH845
B	HOH846
B	HOH847

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA B 704

Chain	Residue
B	ASP613
B	GLU639
D	HOH816
D	HOH917

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA B 705

Chain	Residue
B	ASP614
B	HOH813
D	ASP614

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE TRS B 706

Chain	Residue
B	GLU254
B	ASP258
B	ASP614
B	HOH949
D	GLU254
D	ASP258
D	ASP614
D	HOH914

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE BA D 701

Chain	Residue
D	GLU390
D	HIS395
D	ASP521

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 702

Chain	Residue
D	ASP307
D	PHE478
D	GLU487
D	HOH832
D	HOH833
D	HOH898

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 703

Chain	Residue
C	ILE159
D	VAL329
D	ASP332
D	TYR334
D	GLU336
D	HOH834

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA D 704

Chain	Residue
B	HOH815
B	HOH947
D	ASP613
D	GLU639
D	HOH899

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BA F 701

Chain	Residue
F	GLU390
F	HIS395
F	ASP521
F	HOH876
F	HOH877

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA F 702

Chain	Residue
E	ILE159
F	VAL329
F	ASP332
F	TYR334
F	GLU336
F	HOH817

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA F 703

Chain	Residue
F	ASP307
F	PHE478
F	GLU487
F	HOH836
F	HOH837

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA F 704

Chain	Residue
F	ASP613
F	GLU639

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA F 705

Chain	Residue
F	ASP614
H	ASP614

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA F 706

Chain	Residue
F	GLU254
F	HOH810
H	ASP258
H	HOH911

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA F 707

Chain	Residue
F	ASP616
F	HOH829
F	HOH929
H	ASP255
H	HOH921
H	HOH922

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA F 708

Chain	Residue
F	ASP258
H	GLU254

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BA H 701

Chain	Residue
H	GLU390
H	HIS395
H	ASP521
H	HOH876
H	HOH877

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA H 702

Chain	Residue
G	ILE159
H	VAL329
H	ASP332
H	TYR334
H	GLU336
H	HOH825

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA H 703

Chain	Residue
H	GLU487
H	GOL706
H	HOH839
H	ASP307
H	PHE478

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA H 704

Chain	Residue
H	ASP613
H	GLU639

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG H 705

Chain	Residue
F	ASP614
F	HOH810
F	HOH929
H	GLU254
H	ASP258

site_id	CC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL H 706

Chain	Residue
H	ASP307
H	GLU345
H	PHE478
H	TYR480
H	ASN481
H	VAL482
H	PRO483
H	CA703
H	HOH839

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"10523290","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"23558682","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10523290","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4IEF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PDB","id":"4IEF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 806

Chain	Residue	Details
B	GLU381	electrostatic stabiliser
B	HIS440	proton acceptor, proton donor
B	GLY441	electrostatic stabiliser
B	VAL474	electrostatic stabiliser

site_id	MCSA2
Number of Residues	4
Details	M-CSA 806

Chain	Residue	Details
D	GLU381	electrostatic stabiliser
D	HIS440	proton acceptor, proton donor
D	GLY441	electrostatic stabiliser
D	VAL474	electrostatic stabiliser

site_id	MCSA3
Number of Residues	4
Details	M-CSA 806

Chain	Residue	Details
F	GLU381	electrostatic stabiliser
F	HIS440	proton acceptor, proton donor
F	GLY441	electrostatic stabiliser
F	VAL474	electrostatic stabiliser

site_id	MCSA4
Number of Residues	4
Details	M-CSA 806

Chain	Residue	Details
H	GLU381	electrostatic stabiliser
H	HIS440	proton acceptor, proton donor
H	GLY441	electrostatic stabiliser
H	VAL474	electrostatic stabiliser

246704

PDB entries from 2025-12-24

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