SMTL ID : 1os0.2 (1 other biounit)

Thermolysin with an alpha-amino phosphinic inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 Ligands: 0PQ.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.142, A:H.146, A:E.166, 0PQ.6, 0PQ.6 ZN.8: 5 residues within 4Å: Chain B: H.142, H.146, Y.157, E.166 Ligands: 0PQ.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:H.142, B:H.146, B:E.166, 0PQ.13, 0PQ.13

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.138, A:E.177, A:D.185, A:E.190, H2O.3 CA.3: 6 residues within 4Å: Chain A: E.177, K.182, N.183, 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.1, H2O.5 CA.4: 3 residues within 4Å: Chain A: D.57, D.59, Q.61 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.57, A:D.59, A:Q.61, H2O.3, H2O.5 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:T.194, A:I.197, H2O.5 CA.9: 6 residues within 4Å: Chain B: D.138, E.177, D.185, E.187, E.190 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.138, B:E.177, B:D.185, B:E.190, H2O.10 CA.10: 6 residues within 4Å: Chain B: E.177, K.182, N.183, D.185, E.190 Ligands: CA.9 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.177, B:N.183, B:D.185, B:E.190, H2O.8, H2O.13 CA.11: 3 residues within 4Å: Chain B: D.57, D.59, Q.61 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.57, B:D.59, B:Q.61, H2O.10, H2O.12 CA.12: 4 residues within 4Å: Chain B: Y.193, T.194, I.197, D.200 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.193, B:T.194, B:T.194, B:I.197, H2O.13

2 x 0PQ: N-{(2R)-3-[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine(Non-covalent)

0PQ.6: 18 residues within 4Å: Chain A: Y.110, N.111, N.112, A.113, F.114, F.130, V.139, H.142, E.143, H.146, Y.157, E.166, I.188, G.189, L.202, R.203, H.231 Ligands: ZN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.114, A:F.114, A:V.139, A:I.188, A:L.202, A:L.202 Hydrogen bonds: A:N.112, A:N.112, A:N.112, A:Y.157, A:R.203, A:R.203 Water bridges: A:E.143 Salt bridges: A:H.231 pi-Stacking: A:F.130, A:H.142 0PQ.13: 18 residues within 4Å: Chain B: Y.110, N.111, N.112, A.113, F.114, F.130, V.139, H.142, E.143, H.146, Y.157, E.166, I.188, G.189, L.202, R.203, H.231 Ligands: ZN.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.114, B:F.114, B:V.139, B:I.188, B:L.202, B:L.202 Hydrogen bonds: B:N.112, B:N.112, B:N.112, B:Y.157, B:R.203, B:R.203 Water bridges: B:E.143, B:H.231, B:H.231 Salt bridges: B:H.231 pi-Stacking: B:F.130, B:H.142

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 3 residues within 4Å: Chain A: H.216, S.218, Y.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.218 pi-Cation interactions: A:H.216 DMS.14: 3 residues within 4Å: Chain B: H.216, S.218, Y.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.218 pi-Cation interactions: B:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selkti, M. et al., Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-03-25

Peptides

Thermolysin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thermolysin

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