SMTL ID : 6qf3.1

X-Ray structure of Thermolysin soaked with sodium aspartate on a silicon chip

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: ASP.27, ASP.28 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:E.177, A:E.177, A:D.185, A:E.190 CA.3: 6 residues within 4Å: Chain A: E.177, N.183, P.184, D.185, E.190 Ligands: CA.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.3, H2O.4 CA.4: 3 residues within 4Å: Chain A: D.57, D.59, Q.61 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.4, H2O.5, H2O.14 CA.5: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.193, A:T.194, A:I.197, A:D.200, H2O.3

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.6: 5 residues within 4Å: Chain A: T.293, D.294, L.295, Y.296, G.297 No protein-ligand interaction detected (PLIP)

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

NA.7: 2 residues within 4Å: Chain A: Y.211 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213 NA.8: 6 residues within 4Å: Chain A: F.114, W.115, E.143, H.146 Ligands: EDO.21, ASP.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.115, A:E.143 NA.9: 3 residues within 4Å: Chain A: T.276, S.279, Q.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.276 Water bridges: A:Q.283 NA.10: 5 residues within 4Å: Chain A: H.146, T.149, D.150, N.165 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.146, A:D.150, A:D.150, A:N.165

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

EDO.11: 9 residues within 4Å: Chain A: D.185, W.186, E.187, E.190, G.199, D.200, S.201, K.210, Y.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.185, A:G.199 Water bridges: A:D.185 EDO.12: 7 residues within 4Å: Chain A: G.247, G.248, T.249, S.254, V.255, V.256, G.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.248 Water bridges: A:T.249, A:T.249 EDO.13: 4 residues within 4Å: Chain A: V.7, Y.28, D.59, N.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.28, A:N.60 EDO.14: 3 residues within 4Å: Chain A: I.1, Y.29, L.54 No protein-ligand interaction detected (PLIP) EDO.15: 6 residues within 4Å: Chain A: R.90, Y.151, T.152, A.153, L.271, T.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.152 Water bridges: A:T.272, A:Q.273 EDO.16: 6 residues within 4Å: Chain A: S.245, Q.246, G.259, R.260, D.261, K.262 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.246, A:R.260, A:D.261, A:D.261 Water bridges: A:D.261, A:K.262 EDO.17: 6 residues within 4Å: Chain A: I.1, T.2, G.3, T.23, Q.31, N.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.3, A:G.3 Water bridges: A:T.2 EDO.18: 3 residues within 4Å: Chain A: V.256, G.257, I.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.257 Water bridges: A:G.259 EDO.19: 5 residues within 4Å: Chain A: Y.211, G.212, D.213, I.232 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213 EDO.20: 6 residues within 4Å: Chain A: D.43, K.45, S.53, L.54, W.55, A.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.45, A:A.56 EDO.21: 7 residues within 4Å: Chain A: W.115, H.146, D.150, Y.157 Ligands: NA.8, NA.10, ASP.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.150 EDO.22: 4 residues within 4Å: Chain A: T.299, S.300, Q.301, A.304 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.299, A:Q.301 EDO.23: 7 residues within 4Å: Chain A: E.160, Y.217, F.281, S.282, G.314, V.315, K.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.217, A:S.282, A:K.316 Water bridges: A:Y.217 EDO.24: 2 residues within 4Å: Chain A: I.131, P.195 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.127 EDO.25: 2 residues within 4Å: Chain A: Y.46, Y.66 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.26: 9 residues within 4Å: Chain A: V.13, S.65, Y.66, A.68, P.69, H.105, D.124, I.131, P.132 6 PLIP interactions: 6 interactions with chain A Water bridges: A:G.15, A:Y.46, A:Y.46, A:S.65, A:H.105, A:D.124

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.27: 14 residues within 4Å: Chain A: N.112, A.113, F.114, W.115, H.142, E.143, H.146, Y.157, E.166, H.231 Ligands: ZN.1, NA.8, EDO.21, ASP.28 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.112, A:Y.157, D.28, D.28 Water bridges: A:N.112, A:N.112, A:N.112, A:N.112 Salt bridges: A:H.142, A:H.231 ASP.28: 13 residues within 4Å: Chain A: N.112, A.113, L.133, V.139, H.142, E.143, E.166, I.188, L.202, R.203, H.231 Ligands: ZN.1, ASP.27 10 PLIP interactions: 5 interactions with chain A, 5 Ligand-Ligand interactions Hydrogen bonds: A:A.113, A:R.203, D.27, D.28, D.28, D.28, D.28 Salt bridges: A:H.142, A:R.203, A:H.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieske, J. et al., On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. Iucrj (2019)

Release Date

2019-07-10

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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