SMTL ID : 3t2i.1

Tetragonal thermolysin in the presence of sarcosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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: 6 residues within 4Å: Chain A: E.177, N.183, P.184, 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166 ZN.6: 2 residues within 4Å: Chain A: K.239, H.250 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.250, H2O.1, H2O.1, H2O.1

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

CL.7: 6 residues within 4Å: Chain A: G.12, V.13, L.14, G.15, D.16, K.18 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: 2 residues within 4Å: Chain A: R.285, K.307 Ligand excluded by PLIP

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

NA.10: 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 SAR: SARCOSINE(Non-covalent)

SAR.11: 2 residues within 4Å: Chain A: I.1, Y.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.29 SAR.12: 5 residues within 4Å: Chain A: V.7, N.19, N.21, R.35, Y.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.21, A:N.21 Water bridges: A:D.32 Salt bridges: A:R.35 SAR.13: 1 residues within 4Å: Chain A: R.269 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.269

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

DMS.14: 1 residues within 4Å: Chain A: Y.66 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.66 DMS.15: 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

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