SMTL ID : 3t2h.1

Tetragonal thermolysin in the presence of TMAO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.2 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.2: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.1 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.3 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.2, H2O.3, H2O.3 CA.4: 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

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: H.142, E.143, H.146, Y.157, E.166 Ligands: CL.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166 ZN.6: 5 residues within 4Å: Chain A: K.239, H.250 Ligands: CL.7, CL.9, CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.250

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 8 residues within 4Å: Chain A: D.207, D.215, K.239, H.250 Ligands: ZN.6, CL.9, CL.11, TMO.17 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: H.142, E.143, H.146, Y.157, E.166, H.231 Ligands: ZN.5 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: K.239, T.249, H.250 Ligands: ZN.6, CL.7, CL.11 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: G.12, V.13, L.14, G.15, D.16, K.18, K.182 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: T.249, H.250, Y.251 Ligands: ZN.6, CL.7, CL.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.285, V.289, K.307 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: A.64, S.65 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: S.53, L.54 Ligands: TMO.16 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 2 residues within 4Å: Chain A: Y.211, D.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213

3 x TMO: trimethylamine oxide(Non-covalent)

TMO.16: 3 residues within 4Å: Chain A: I.1, Y.29 Ligands: CL.14 No protein-ligand interaction detected (PLIP) TMO.17: 4 residues within 4Å: Chain A: S.206, D.207, K.239 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.207 TMO.18: 5 residues within 4Å: Chain A: F.114, W.115, E.143, H.146, Y.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.115, A:W.115 Salt bridges: A:E.143 pi-Cation interactions: A:Y.157

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

DMS.19: 1 residues within 4Å: Chain A: Y.66 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.46 pi-Cation interactions: A:Y.66 DMS.20: 1 residues within 4Å: Chain A: Y.151 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marshall, H. et al., The use of trimethylamine N-oxide as a primary precipitating agent and related methylamine osmolytes as cryoprotective agents for macromolecular crystallography. Acta Crystallogr.,Sect.D (2012)

Release Date

2011-12-28

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Thermolysin

Related Entries With Identical Sequence