SMTL ID : 3msa.1

Crystal structure of Thermolysin in complex with 3-Bromophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

2 x B3R: 3-bromophenol(Non-covalent)

B3R.1: 10 residues within 4Å: Chain A: N.112, A.113, F.130, L.133, V.139, H.142, E.143, I.188, G.189, L.202 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.130, A:L.133, A:V.139, A:V.139 Hydrogen bonds: A:H.142, A:E.143 Water bridges: A:R.203 Halogen bonds: A:I.188 B3R.2: 9 residues within 4Å: Chain A: A.77, Y.81, Y.84, S.92, Y.93, I.100, L.144, T.145, V.148 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.84, A:Y.93, A:L.144, A:V.148 Hydrogen bonds: A:L.144, A:V.148 Halogen bonds: A:A.77

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.142, E.143, H.146, E.166 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.142, A:H.146, A:E.166, H2O.7

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.5 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.5: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.4 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.3, H2O.6 CA.6: 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.3, H2O.3, H2O.7 CA.7: 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.7, H2O.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: V.13, I.131, P.132 No protein-ligand interaction detected (PLIP) GOL.9: 4 residues within 4Å: Chain A: F.114, W.115, N.116 Ligands: IPA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.115 Water bridges: A:W.115

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.10: 5 residues within 4Å: Chain A: F.114, W.115, E.143, H.146 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Behnen, J. et al., Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Chemmedchem (2012)

Release Date

2011-05-11

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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