SMTL ID : 6n4w.1

Tetragonal thermolysin (with 50% xylose) cryocooled in a nitrogen gas stream to 100 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: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: ZN.6 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.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.3, H2O.6, H2O.13 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: 6 residues within 4Å: Chain A: H.142, E.143, H.146, E.166 Ligands: ZN.7, 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.5: 4 residues within 4Å: Chain A: K.239, H.250, Y.251 Ligands: ZN.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, H2O.11 ZN.6: 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.7: 4 residues within 4Å: Chain A: E.166, H.231 Ligands: ZN.4, 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.8: 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.9: 5 residues within 4Å: Chain A: A.113, H.142, E.143 Ligands: ZN.4, ZN.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.143, H2O.6, H2O.10, H2O.11, H2O.14 ZN.10: 5 residues within 4Å: Chain A: K.239, Y.242, L.243, H.250 Ligands: ZN.5 No protein-ligand interaction detected (PLIP)

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

XYP.11: 6 residues within 4Å: Chain A: I.1, Y.29, G.52, S.53, L.54 Ligands: XYS.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: A:Y.29, A:G.52, A:S.53 XYP.12: 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:K.219, A:Y.251 Salt bridges: A:H.216 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.11, A:F.63 Water bridges: A:R.11, A:R.11, A:V.13, A:L.14 Salt bridges: A:R.11 XYP.14: 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.15: 2 residues within 4Å: Chain A: Q.273, Y.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.273 XYP.16: 7 residues within 4Å: Chain A: I.1, T.2, G.3, S.5, T.23, Q.31, N.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.1, A:G.3, A:Q.31 Water bridges: A:N.33, A:N.37 XYP.17: 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:Q.283 XYP.18: 4 residues within 4Å: Chain A: D.294, L.295, Y.296, G.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.295 Water bridges: A:T.293, A:D.294, A:S.298 XYP.19: 4 residues within 4Å: Chain A: R.11, Q.17, Q.61, F.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.61 Salt bridges: A:R.11

2 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.20: 2 residues within 4Å: Chain A: D.150, Y.151 No protein-ligand interaction detected (PLIP) XYS.21: 5 residues within 4Å: Chain A: K.45, T.49, G.52, S.53 Ligands: XYP.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.52

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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