SMTL ID : 6qf2.1

X-Ray structure of Thermolysin crystallized on a silicon chip

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 Ligands: LEU.6, ZN.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166, H2O.2 ZN.8: 4 residues within 4Å: Chain A: Y.157, E.166, H.231 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.157, A:E.166, A:H.231, H2O.2, H2O.6

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.2, H2O.6 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.6, H2O.13 CA.5: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.193, A:I.197, A:D.200, H2O.2, H2O.12

1 x LEU: LEUCINE(Non-covalent)

LEU.6: 15 residues within 4Å: Chain A: N.112, A.113, F.114, F.130, L.133, V.139, H.142, E.143, I.188, G.189, L.202, R.203, H.231 Ligands: ZN.1, LYS.7 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.133, A:V.139, A:L.202 Hydrogen bonds: A:N.112, A:R.203, A:R.203 Water bridges: L.6, K.7

1 x LYS: LYSINE(Non-covalent)

LYS.7: 7 residues within 4Å: Chain A: N.111, N.112, F.130, L.202, R.203, H.231 Ligands: LEU.6 9 PLIP interactions: 5 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.111, A:N.112, A:N.112, A:N.112, K.7 Salt bridges: A:H.231, K.7 Water bridges: L.6, L.6

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

NA.9: 1 residues within 4Å: Chain A: Y.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.211

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

EDO.10: 7 residues within 4Å: Chain A: G.247, G.248, T.249, S.254, V.255, V.256, G.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.248 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.185, A:G.199, A:K.210 Water bridges: A:D.185 EDO.12: 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.13: 4 residues within 4Å: Chain A: Q.246, G.259, R.260, D.261 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.246, A:R.260, A:D.261, A:D.261 Water bridges: A:R.260, A:D.261, A:K.262 EDO.14: 4 residues within 4Å: Chain A: Y.274, A.286, A.287, Q.290 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.283, A:A.287 EDO.15: 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.16: 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:N.33 EDO.17: 4 residues within 4Å: Chain A: A.209, K.210, Y.211, G.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.210

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.18: 5 residues within 4Å: Chain A: T.293, D.294, L.295, Y.296, G.297 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 9 residues within 4Å: Chain A: V.13, Y.46, S.65, Y.66, A.68, P.69, H.105, D.124, P.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.13 Water bridges: A:S.65

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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