SMTL ID : 1qf1.1

THERMOLYSIN (E.C.3.4.24.27) COMPLEXED WITH (2-SULPHANYLHEPTANOYL)-PHE-ALA. PARAMETERS FOR ZN-BIDENTATION OF MERCAPTOACYLDIPEPTIDES IN METALLOENDOPEPTIDASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 Ligands: TI1.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166

4 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.1 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.2 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.59, A:Q.61, H2O.1, H2O.1, H2O.2 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.1

1 x TI1: [2(R,S)-2-SULFANYLHEPTANOYL]-PHE-ALA(Non-covalent)

TI1.6: 18 residues within 4Å: Chain A: Y.110, N.112, A.113, F.114, L.133, 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, DMS.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.133, A:V.139, A:V.139, A:I.188, A:L.202 Hydrogen bonds: A:N.112, A:N.112, A:A.113, A:R.203, A:R.203 Salt bridges: A:H.231 pi-Stacking: A:H.142

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

DMS.7: 4 residues within 4Å: Chain A: W.115, H.146, Y.157 Ligands: TI1.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.165 pi-Cation interactions: A:H.146, A:Y.157 DMS.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaucher, J.F. et al., Crystal structures of alpha-mercaptoacyldipeptides in the thermolysin active site: structural parameters for a Zn monodentation or bidentation in metalloendopeptidases. Biochemistry (1999)

Release Date

1999-12-29

Peptides

PROTEIN (THERMOLYSIN): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PROTEIN (THERMOLYSIN)

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