SMTL ID : 6i9a.1 (1 other biounit)

Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.1: 4 residues within 4Å: Chain A: E.319, N.323, R.369, S.441 No protein-ligand interaction detected (PLIP) UNX.2: 3 residues within 4Å: Chain A: D.43, H.45, K.66 No protein-ligand interaction detected (PLIP)

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

NA.3: 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:T.316 NA.4: 5 residues within 4Å: Chain A: Y.174, V.293, T.308, S.309, D.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.174, A:T.308

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.5 CA.6: 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.13, H2O.16

1 x H8E: benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate(Non-covalent)

H8E.7: 16 residues within 4Å: Chain A: W.163, T.214, A.215, H.216, G.217, A.223, N.247, C.248, C.249, I.250, N.282, S.283, Y.284, W.285, D.288, H.347 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.163, A:H.216, A:A.223, A:I.250, A:W.285 Hydrogen bonds: A:T.214, A:A.215, A:G.217, A:G.217, A:C.249, A:N.282, A:S.283, A:W.285, A:D.288, A:D.288

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 6 residues within 4Å: Chain A: R.15, Y.41, L.42, V.407, L.408, K.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.15, A:R.15

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: Q.387, S.389, Y.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.389 GOL.10: 6 residues within 4Å: Chain A: Y.10, D.320, S.321, N.323, M.366, S.441 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.320, A:N.323 Water bridges: A:D.320, A:Y.322, A:N.323 GOL.11: 6 residues within 4Å: Chain A: Y.201, S.202, N.205, Q.231, A.234, L.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.201, A:N.205, A:Q.231 Water bridges: A:Y.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guevara, T. et al., Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor. Sci Rep (2019)

Release Date

2019-03-13

Peptides

Lys-gingipain W83: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lys-gingipain W83

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