SMTL ID : 3ls7.1

Crystal structure of Thermolysin in complex with Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x XE: XENON(Non-covalent)

XE.1: 3 residues within 4Å: Chain A: Y.84, S.92, Y.93 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.1, H2O.1, H2O.4 CA.3: 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.1, H2O.1 CA.4: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.5 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.8 CA.5: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, 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

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 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.8

1 x VAL: VALINE(Non-covalent)

VAL.7: 8 residues within 4Å: Chain A: N.112, A.113, V.139, E.143, L.202, R.203, H.231 Ligands: LYS.8 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:V.139, K.8 Hydrogen bonds: A:E.143, A:R.203, A:R.203, K.8

1 x LYS: LYSINE(Non-covalent)

LYS.8: 7 residues within 4Å: Chain A: N.111, N.112, F.130, L.202, R.203, H.231 Ligands: VAL.7 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.202, V.7 Hydrogen bonds: A:N.111, A:N.112, A:N.112 Salt bridges: A:H.231

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: W.115, H.146, D.150, Y.157, N.165 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.165, A:N.165 Water bridges: A:W.115 GOL.10: 4 residues within 4Å: Chain A: G.109, Y.110, N.111, N.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.109, A:N.111, A:N.112 GOL.11: 5 residues within 4Å: Chain A: G.248, T.249, S.254, V.255, V.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.249, A:T.249, A:V.255 GOL.12: 2 residues within 4Å: Chain A: Y.157 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.115 GOL.13: 4 residues within 4Å: Chain A: G.36, N.37, N.96, N.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.97 GOL.14: 4 residues within 4Å: Chain A: Y.42, P.51, R.101, Q.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.119

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

DMS.15: 3 residues within 4Å: Chain A: H.216, S.218, Y.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.218 pi-Cation interactions: A:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Behnen, J. et al., Old acquantance rediscovered, use of xenon/protein complexes as a generic tool for SAD phasing of in house data. To be Published

Release Date

2011-02-23

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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