SMTL ID : 5js3.1

Thermolysin in complex with JC114.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: 6MG.11 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.4 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: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.4, H2O.4, H2O.12 CA.4: 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.4 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.5, H2O.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: F.114, W.115, E.143, H.146, Y.157, N.165 Ligands: 6MG.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.115, A:W.115, A:E.143 Water bridges: A:H.146, A:H.146, A:D.150 GOL.7: 4 residues within 4Å: Chain A: G.109, Y.110, N.111, N.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.109, A:N.111, A:N.111, A:N.112 Water bridges: A:N.111

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

DMS.8: 4 residues within 4Å: Chain A: H.216, S.218, K.219, Y.251 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:H.216, A:Y.251 DMS.9: 6 residues within 4Å: Chain A: I.1, T.2, G.3, S.5, Q.31, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.3 DMS.10: 4 residues within 4Å: Chain A: Y.110, N.112, F.114 Ligands: 6MG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.110 pi-Cation interactions: A:F.114

1 x 6MG: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2,3,3-trimethylbutyl]-L-leucinamide(Non-covalent)

6MG.11: 21 residues within 4Å: Chain A: N.111, N.112, A.113, F.114, W.115, N.116, F.130, 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, GOL.6, DMS.10 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.114, A:L.133, A:V.139, A:L.202, A:L.202, A:H.231 Hydrogen bonds: A:N.112, A:N.112, A:E.143, A:E.143, A:Y.157, A:Y.157, A:R.203, A:R.203, A:H.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krimmer, S.G. et al., Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands. J. Med. Chem. (2016)

Release Date

2016-12-21

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Thermolysin

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