SMTL ID : 4ief.3 (3 other biounits)

Complex of Porphyromonas gingivalis RgpB pro- and mature domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BA: BARIUM ION(Non-covalent)

BA.1: 3 residues within 4Å: Chain B: E.161, H.166, D.292 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.161, B:H.166, B:D.292, H2O.6, H2O.6

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: I.140 Chain B: V.100, D.103, Y.105, E.107 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:V.100, B:Y.105, B:E.107, A:I.140, H2O.4 CA.3: 3 residues within 4Å: Chain B: D.78, F.249, E.258 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.78, B:D.78, B:E.258, B:E.258, H2O.5 CA.4: 2 residues within 4Å: Chain B: D.384, E.410 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.384, B:D.384, B:E.410, B:E.410 CA.5: 2 residues within 4Å: Chain B: D.385, T.414 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.385

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain B: E.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.25 NA.7: 2 residues within 4Å: Chain B: D.384, D.387 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.387 NA.8: 1 residues within 4Å: Chain B: D.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Diego, I. et al., Porphyromonas gingivalis Virulence Factor Gingipain RgpB Shows a Unique Zymogenic Mechanism for Cysteine Peptidases. J.Biol.Chem. (2013)

Release Date

2013-04-10

Peptides

Gingipain R2 Pro-Domain: A
Gingipain R2 Mature Domain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Gingipain R2 Pro-Domain

Gingipain R2 Mature Domain

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