SMTL ID : 4rbm.1

Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.85, F.254, E.263 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.254, A:E.263, A:E.263, H2O.2, H2O.3 CA.2: 4 residues within 4Å: Chain A: D.109, D.111, F.113, E.115 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.109, A:D.111, A:F.113, A:E.115, H2O.2

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

NA.3: 5 residues within 4Å: Chain A: Y.174, V.293, T.308, S.309, D.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.174 NA.4: 7 residues within 4Å: Chain A: A.315, T.316, L.318, S.321, Y.322, N.323, R.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.315 NA.6: 2 residues within 4Å: Chain A: T.187 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.187

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 3 residues within 4Å: Chain A: E.151 Ligands: HIS.7, ACT.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.151, A:E.151, HIS.7

1 x HIS: HISTIDINE(Non-covalent)

HIS.7: 4 residues within 4Å: Chain A: E.151, M.371 Ligands: NI.5, ACT.8 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 4 residues within 4Å: Chain A: E.151, T.187 Ligands: NI.5, HIS.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.187 Salt bridges: H.7 ACT.9: 4 residues within 4Å: Chain A: E.128, K.233, R.267, V.268 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.267 Water bridges: A:K.233 Salt bridges: A:K.233

3 x AZI: AZIDE ION(Non-covalent)

AZI.10: 2 residues within 4Å: Chain A: H.6, D.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.6, A:D.111 AZI.11: 4 residues within 4Å: Chain A: H.6, G.7, L.9, W.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.6, A:G.7 AZI.12: 3 residues within 4Å: Chain A: D.160, S.162, H.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.216 Water bridges: A:Y.161

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: K.60, E.92, Y.104 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.60, A:E.92, A:K.95 Water bridges: A:H.64, A:E.92 GOL.14: 7 residues within 4Å: Chain A: V.189, Y.190, N.191, Y.192, H.203 Ligands: GOL.15, GOL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.191, A:N.191 GOL.15: 7 residues within 4Å: Chain A: N.191, Y.192, L.193, K.194, A.195, P.196 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.193, A:K.194 Water bridges: A:P.196 GOL.16: 6 residues within 4Å: Chain A: T.187, D.188, V.189, Y.190 Ligands: NA.6, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.187, A:V.189

1 x CKC: (3S)-3,7-diaminoheptan-2-one(Covalent)

CKC.17: 10 residues within 4Å: Chain A: T.214, A.215, H.216, G.217, N.247, C.248, C.249, S.283, W.285, D.288 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.285, A:W.285 Hydrogen bonds: A:T.214, A:T.214, A:H.216, A:G.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Diego, I. et al., Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis. J.Biol.Chem. (2014)

Release Date

2014-10-08

Peptides

Lys-gingipain W83: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lys-gingipain W83

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