SMTL ID : 1cvr.1

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x H37: D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-OXOHEXAN-3-YL]-L-PHENYLALANINAMIDE(Covalent)

H37.1: 12 residues within 4Å: Chain A: D.163, T.209, G.210, H.211, G.212, V.242, C.244, D.281, Q.282, Y.283, W.284, M.288 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.281, A:Y.283, A:W.284 Hydrogen bonds: A:G.210, A:G.212, A:C.244, A:Q.282, A:W.284, A:W.284 Salt bridges: A:D.163 pi-Cation interactions: A:W.284, A:W.284

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.161, H.166, D.292 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.161, A:H.166, A:D.292, H2O.5, H2O.9, H2O.11 CA.3: 3 residues within 4Å: Chain A: D.78, F.249, E.258 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.78, A:D.78, A:E.258, A:E.258, H2O.3 CA.4: 4 residues within 4Å: Chain A: V.100, D.103, Y.105, E.107 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.100, A:D.103, A:Y.105, A:E.107, H2O.5 CA.5: 3 residues within 4Å: Chain A: E.293, E.296, H.302 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.293, A:E.293, A:E.296, A:H.302, H2O.1 CA.6: 1 residues within 4Å: Chain A: H.221 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.221, H2O.3 CA.8: 1 residues within 4Å: Chain A: E.119 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.119, A:E.119, H2O.5, H2O.13

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: E.152, H.211, W.284 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.152, A:H.211, H2O.5, H2O.13 ZN.9: 2 residues within 4Å: Chain A: H.130, N.134 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.130, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eichinger, A. et al., Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold. EMBO J. (1999)

Release Date

2000-03-01

Peptides

GINGIPAIN R: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GINGIPAIN R