SMTL ID : 9ozy.1

Gradient equilibration of hexagonal thermolysin to low salt over 15 minutes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x VAL: VALINE(Non-covalent)

VAL.1: 13 residues within 4Å: Chain A: N.112, A.113, F.130, L.133, V.139, H.142, E.143, I.188, L.202, R.203, H.231 Ligands: LYS.2, ZN.7 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.133, A:L.202 Hydrogen bonds: A:N.112, A:R.203, A:R.203, K.2

1 x LYS: LYSINE(Non-covalent)

LYS.2: 7 residues within 4Å: Chain A: N.111, N.112, F.130, L.202, R.203, H.231 Ligands: VAL.1 8 PLIP interactions: 5 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.202 Hydrogen bonds: A:N.111, A:N.112, A:N.112 Salt bridges: A:H.231, K.2 Water bridges: V.1, K.2

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 7 residues within 4Å: Chain A: E.177, K.182, N.183, P.184, D.185, E.190 Ligands: CA.3 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.5: 4 residues within 4Å: Chain A: D.57, D.59, Q.61, F.62 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.59, A:Q.61, H2O.2, H2O.2, H2O.8 CA.6: 5 residues within 4Å: Chain A: Y.193, T.194, I.197, S.198, 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 ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 Ligands: VAL.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166, H2O.7

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

DMS.8: 4 residues within 4Å: Chain A: H.216, S.218, K.219, Y.251 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., Automated gradient equilibration of macromolecular crystals to new solution conditions. Acta Crystallogr.,Sect.F (2025)

Release Date

2025-10-15

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Thermolysin

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