SMTL ID : 4tkx.1

Structure of Protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: E.319, R.369, K.373, N.442 Ligands: EDO.12, EDO.13 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.319, A:E.319, A:N.442 Water bridges: A:R.369, A:R.369, A:R.369, A:R.369, A:R.369, A:K.373, A:K.373 Salt bridges: A:R.369, A:K.373 SO4.2: 5 residues within 4Å: Chain A: A.195, P.196, Y.197, T.198 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.197, A:T.198 Water bridges: A:D.224 SO4.3: 5 residues within 4Å: Chain A: D.1, V.2, H.338, N.341, I.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.2, A:N.341 Salt bridges: A:H.338 SO4.4: 7 residues within 4Å: Chain A: T.198, G.199, C.200, Y.201, S.202 Ligands: EDO.9, EDO.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.199, A:C.200, A:Y.201, A:S.202, A:S.202, A:S.202

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

NA.5: 8 residues within 4Å: Chain A: A.315, T.316, F.317, L.318, S.321, Y.322, N.323, R.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.321 NA.6: 9 residues within 4Å: Chain A: Y.174, V.293, G.294, F.305, T.308, S.309, M.310, G.311, D.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.309, A:G.311

1 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain A: D.160, W.163, H.216, W.285 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.160, H2O.1

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

ACT.8: 4 residues within 4Å: Chain A: E.51, S.58, A.61, F.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.58, A:F.62 Water bridges: A:S.58

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 8 residues within 4Å: Chain A: Y.201, S.202, L.204, N.205, L.227, Q.231, L.235 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.202, A:S.202, A:Q.231 EDO.10: 7 residues within 4Å: Chain A: E.128, N.131, K.233, V.264, R.267, V.268, K.269 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.233 EDO.11: 8 residues within 4Å: Chain A: N.296, A.297, V.298, V.301, P.303, T.304, G.307, T.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.304, A:T.304, A:T.304 EDO.12: 9 residues within 4Å: Chain A: H.184, G.185, R.369, A.370, M.371, P.372, K.373, N.442 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.373, A:N.442 EDO.13: 3 residues within 4Å: Chain A: H.184, E.319 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.184, A:E.319 EDO.14: 7 residues within 4Å: Chain A: Y.3, N.296, T.308, S.309, M.310, H.338, I.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.296, A:H.338 EDO.15: 5 residues within 4Å: Chain A: K.152, D.188, Y.190, H.203, T.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.188 Water bridges: A:Y.190, A:Y.190 EDO.16: 9 residues within 4Å: Chain A: Y.197, T.198, G.199, C.200, Y.201, P.225, L.226 Ligands: SO4.2, SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.199 EDO.17: 4 residues within 4Å: Chain A: D.8, L.9, Y.10, N.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.9 EDO.18: 7 residues within 4Å: Chain A: D.134, K.135, M.138, K.238, D.239, Y.241, E.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.134, A:D.239, A:Y.241 Water bridges: A:E.270, A:E.270

1 x PB: LEAD (II) ION(Non-covalent)

PB.19: 7 residues within 4Å: Chain A: D.85, S.122, F.254, D.255, P.259, E.263, R.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.254, A:E.263, A:E.263, H2O.17, H2O.19

1 x TCK: N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide(Covalent)

TCK.20: 12 residues within 4Å: Chain A: T.214, A.215, H.216, G.217, N.247, C.248, C.249, N.282, S.283, Y.284, W.285, D.288 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.284, A:W.285 Hydrogen bonds: A:A.215, A:G.217, A:C.249, A:S.283, A:W.285, A:D.288 Water bridges: A:T.214, A:T.214, A:W.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health. Protein Sci. (2015)

Release Date

2014-12-31

Peptides

Lys-gingipain W83: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

Lys-gingipain W83