SMTL ID : 6fsm.1

Crystal structure of TCE-treated Thermolysin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: PO4.6, VAL.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: CA.3 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.3: 6 residues within 4Å: Chain A: E.177, N.183, P.184, D.185, E.190 Ligands: CA.2 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.4 CA.4: 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.4, H2O.4, H2O.9 CA.5: 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.3, H2O.9

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 14 residues within 4Å: Chain A: N.112, A.113, F.114, W.115, H.142, E.143, H.146, Y.157, E.166, H.231 Ligands: ZN.1, GOL.7, VAL.10, LYS.11 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:A.113, A:A.113, A:Y.157, V.10, K.11, K.11 Salt bridges: A:H.142, A:H.146, A:H.231

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: W.115, H.146, T.149, D.150, Y.157, N.165 Ligands: PO4.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.146, A:D.150, A:D.150, A:N.165 Water bridges: A:W.115 GOL.8: 6 residues within 4Å: Chain A: G.247, G.248, T.249, S.254, V.255, V.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.248, A:V.255, A:V.255 Water bridges: A:G.247, A:T.249 GOL.9: 5 residues within 4Å: Chain A: G.109, Y.110, N.111, N.112 Ligands: LYS.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.111, A:N.111, A:N.112, K.11

1 x VAL: VALINE(Non-covalent)

VAL.10: 14 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: ZN.1, PO4.6, LYS.11 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.133, A:L.202 Hydrogen bonds: A:N.112, A:A.113, A:R.203, A:R.203, K.11

1 x LYS: LYSINE(Non-covalent)

LYS.11: 10 residues within 4Å: Chain A: N.111, N.112, T.129, F.130, L.202, R.203, H.231 Ligands: PO4.6, GOL.9, VAL.10 9 PLIP interactions: 3 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: K.11, K.11, A:N.111, A:N.112, A:N.112, A:N.112 Salt bridges: K.11, A:H.231 Hydrophobic interactions: A:L.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pichlo, C. et al., Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-05-02

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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