SMTL ID : 5a3y.1

SAD structure of Thermolysin obtained by multi crystal data collection

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x VAL: VALINE(Non-covalent)

VAL.1: 8 residues within 4Å: Chain A: N.344, A.345, L.365, E.375, L.434, R.435, H.463 Ligands: LYS.2 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.365, A:L.434, K.2 Hydrogen bonds: A:E.375, A:R.435, A:R.435, K.2 Water bridges: A:N.344, V.1

1 x LYS: LYSINE(Non-covalent)

LYS.2: 5 residues within 4Å: Chain A: N.343, N.344, F.362, H.463 Ligands: VAL.1 10 PLIP interactions: 6 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:F.362, V.1 Hydrogen bonds: A:N.344, A:N.344 Water bridges: A:H.463, A:H.463, V.1, V.1, V.1 Salt bridges: A:H.463

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.374, H.378, Y.389, E.398 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.374, A:H.378, A:E.398, H2O.8

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.370, E.409, D.417, E.419, E.422 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.370, A:E.409, A:E.409, A:D.417, A:E.422 CA.5: 5 residues within 4Å: Chain A: E.409, N.415, D.417, E.422 Ligands: CA.4 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.409, A:N.415, A:D.417, A:E.422, H2O.9, H2O.9 CA.6: 3 residues within 4Å: Chain A: D.289, D.291, Q.293 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.289, A:D.291, A:Q.293, H2O.4, H2O.4 CA.7: 4 residues within 4Å: Chain A: Y.425, T.426, I.429, D.432 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.425, A:I.429, A:D.432, H2O.9, H2O.9

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

DMS.8: 3 residues within 4Å: Chain A: H.448, S.450, Y.483 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.450 pi-Cation interactions: A:H.448, A:Y.483

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.9: 4 residues within 4Å: Chain A: Y.325, G.349, S.350, Y.383 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.325 TMO.10: 1 residues within 4Å: Chain A: Y.383 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zander, U. et al., Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-11-11

Peptides

THERMOLYSIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

THERMOLYSIN