SMTL ID : 5uu9.1

Tetragonal thermolysin cryocooled to 100 K with 40% xylose as cryoprotectant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: ZN.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.6 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.4, H2O.5, H2O.12 CA.4: 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.2, H2O.11

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: E.177, N.183, P.184, D.185, E.190, D.191 Ligands: CA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.2 ZN.5: 7 residues within 4Å: Chain A: H.142, E.143, H.146, Y.157, E.166 Ligands: ZN.6, ZN.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.142, A:H.146, A:E.166, H2O.9 ZN.6: 5 residues within 4Å: Chain A: Y.157, E.166, H.231 Ligands: ZN.5, ZN.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.231, H2O.9, H2O.9, H2O.13 ZN.7: 5 residues within 4Å: Chain A: A.113, H.142, E.143 Ligands: ZN.5, ZN.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.143, H2O.4, H2O.9, H2O.13

8 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.8: 5 residues within 4Å: Chain A: Y.274, Q.283, A.286, A.287, Q.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.283, A:A.287 XYP.9: 9 residues within 4Å: Chain A: N.159, E.160, Y.217, R.220, Y.221, T.222, G.223, G.228, N.233 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.160, A:Y.217, A:Y.217, A:G.228, A:N.233 Water bridges: A:N.159, A:R.220, A:R.220, A:T.222 Salt bridges: A:R.220 XYP.10: 6 residues within 4Å: Chain A: D.185, W.186, S.206, Y.242, Q.246 Ligands: DMS.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.246 Water bridges: A:W.186, A:W.186, A:W.186, A:S.206 XYP.11: 4 residues within 4Å: Chain A: H.216, S.218, K.219, Y.251 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.216, A:S.218, A:Y.251 Salt bridges: A:H.216 XYP.12: 7 residues within 4Å: Chain A: Y.83, V.87, L.175, F.178, Y.179, R.260, D.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.175, A:R.260, A:R.260, A:D.261 Water bridges: A:D.261 XYP.13: 9 residues within 4Å: Chain A: R.11, G.12, V.13, L.14, G.15, F.63, A.64, S.65, A.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.11, A:R.11, A:F.63 Water bridges: A:G.15 Salt bridges: A:R.11 XYP.14: 4 residues within 4Å: Chain A: A.209, K.210, Y.211, G.212 No protein-ligand interaction detected (PLIP) XYP.15: 8 residues within 4Å: Chain A: I.1, T.2, G.3, T.4, S.5, T.23, Q.31, N.33 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.3, A:G.3, A:S.5, A:Q.31 Water bridges: A:I.1, A:I.1

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

DMS.16: 5 residues within 4Å: Chain A: S.206, D.207, K.239, Y.242 Ligands: XYP.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.239 Water bridges: A:Y.242, A:H.250, A:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Acta Crystallogr D Struct Biol (2018)

Release Date

2017-03-08

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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