SMTL ID : 6n4z.1

Tetragonal thermolysin (with 50% xylose) plunge cooled in liquid nitrogen to 77 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.5, H2O.13 CA.2: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: ZN.7 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: 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.3

7 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: K.239, H.250, Y.251 Ligands: ZN.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.250, H2O.2, H2O.13, H2O.13 ZN.5: 6 residues within 4Å: Chain A: H.142, E.143, H.146, E.166 Ligands: ZN.8, ZN.9 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.10 ZN.6: 2 residues within 4Å: Chain A: D.226, H.231 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.226, A:H.231 ZN.7: 6 residues within 4Å: Chain A: E.177, N.183, P.184, D.185, E.190 Ligands: CA.2 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.1 ZN.8: 4 residues within 4Å: Chain A: E.166, H.231 Ligands: ZN.5, ZN.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.231, H2O.10, H2O.10, H2O.14 ZN.9: 5 residues within 4Å: Chain A: A.113, H.142, E.143 Ligands: ZN.5, ZN.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.143, H2O.4, H2O.10, H2O.10, H2O.14 ZN.10: 4 residues within 4Å: Chain A: K.239, Y.242, L.243 Ligands: ZN.4 No protein-ligand interaction detected (PLIP)

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

XYP.11: 2 residues within 4Å: Chain A: Y.46, Y.66 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.46 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: N.159, E.160, Y.217, R.220, Y.221, T.222, G.223, G.228, N.233 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.159, A:E.160, A:E.160, A:Y.217, A:G.228, A:N.233 Water bridges: A:T.222 Salt bridges: A:R.220 XYP.14: 3 residues within 4Å: Chain A: A.209, K.210, G.212 No protein-ligand interaction detected (PLIP) XYP.15: 7 residues within 4Å: Chain A: Y.274, L.275, Q.283, L.284, A.286, A.287, Q.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.283, A:A.287 Water bridges: A:Y.274 XYP.16: 7 residues within 4Å: Chain A: I.1, T.2, G.3, S.5, T.23, Q.31, N.33 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.1, A:G.3, A:Q.31 Water bridges: A:I.1, A:S.5, A:N.33 XYP.17: 6 residues within 4Å: Chain A: A.44, K.45, R.47, T.49, G.52, S.53 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.44, A:K.45, A:G.52 Water bridges: A:R.47, A:T.49, A:T.49, A:T.49, A:G.52, A:S.53, A:S.53, A:S.53, A:S.53 Salt bridges: A:R.47 XYP.18: 9 residues within 4Å: Chain A: R.11, G.12, V.13, L.14, G.15, F.63, A.64, S.65, A.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.11, A:R.11, A:A.64 Salt bridges: A:R.11 XYP.19: 2 residues within 4Å: Chain A: D.150, Y.151 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, K. et al., A comparison of gas stream cooling and plunge cooling of macromolecular crystals. J.Appl.Crystallogr. (2019)

Release Date

2019-10-02

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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