SMTL ID : 4mwp.1

Thermolysin in complex with UBTLN46

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.23 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: 2GC.13 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: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.5 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: 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.1, H2O.2 CA.4: 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.4 CA.5: 5 residues within 4Å: Chain A: E.177, 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.3, H2O.15

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

DMS.6: 5 residues within 4Å: Chain A: I.1, T.2, G.3, Q.31, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.3 DMS.7: 5 residues within 4Å: Chain A: Y.110, N.112, F.114 Ligands: GOL.10, 2GC.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.110 pi-Cation interactions: A:F.114 DMS.8: 1 residues within 4Å: Chain A: G.95 No protein-ligand interaction detected (PLIP) DMS.9: 1 residues within 4Å: Chain A: Y.66 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.66

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: G.109, Y.110, N.111, N.112 Ligands: DMS.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.109, A:N.111, A:N.111, A:N.112 GOL.11: 6 residues within 4Å: Chain A: F.114, W.115, E.143, H.146, Y.157 Ligands: 2GC.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.115, A:E.143 Water bridges: A:D.150, A:N.165 GOL.12: 4 residues within 4Å: Chain A: Q.273, Y.274, L.275, T.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.273 Water bridges: A:Y.274

1 x 2GC: P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-4-methyl-1-oxo-1-(phenethylamino)pentan-2-yl)phosphonamidic acid(Non-covalent)

2GC.13: 19 residues within 4Å: Chain A: N.112, A.113, F.114, W.115, N.116, L.133, V.139, H.142, E.143, H.146, Y.157, E.166, I.188, L.202, R.203, H.231 Ligands: ZN.1, DMS.7, GOL.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.114, A:L.133, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krimmer, S.G. et al., Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors. Chemmedchem (2014)

Release Date

2014-04-02

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Thermolysin

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