SMTL ID : 5uub.1

Tetragonal thermolysin cryocooled to 100 K with 25% xylose/25% mpd 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: 5 interactions with chain A Metal complexes: A:D.138, A:E.177, A:E.177, A:D.185, A:E.190 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.2, H2O.6, 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.3, H2O.10

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: E.177, K.182, N.183, P.184, D.185, E.190 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: 8 residues within 4Å: Chain A: H.142, E.143, H.146, Y.157, E.166 Ligands: ZN.6, ZN.7, MRD.20 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.142, A:H.146, A:E.166, H2O.10 ZN.6: 6 residues within 4Å: Chain A: Y.157, E.166, H.231 Ligands: ZN.5, ZN.7, MRD.20 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.231, H2O.1, H2O.2, H2O.10 ZN.7: 6 residues within 4Å: Chain A: A.113, H.142, E.143 Ligands: ZN.5, ZN.6, MRD.20 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.143, H2O.1, H2O.3, H2O.10 ZN.8: 3 residues within 4Å: Chain A: D.226, V.230, H.231 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.226, A:D.226, A:H.231 ZN.9: 8 residues within 4Å: Chain A: S.206, K.239, Y.242, L.243 Ligands: ZN.10, CL.11, CL.12, CL.13 No protein-ligand interaction detected (PLIP) ZN.10: 7 residues within 4Å: Chain A: K.239, T.249, H.250, Y.251 Ligands: ZN.9, CL.13, CL.14 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, H2O.9

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 8 residues within 4Å: Chain A: K.239, Y.242, L.243, G.247, G.248, T.249 Ligands: ZN.9, CL.12 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: S.206, K.239 Ligands: ZN.9, CL.11, CL.13 Ligand excluded by PLIP CL.13: 8 residues within 4Å: Chain A: D.207, D.215, K.239, H.250 Ligands: ZN.9, ZN.10, CL.12, CL.14 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: T.249, H.250, Y.251 Ligands: ZN.10, CL.13 Ligand excluded by PLIP

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.15: 8 residues within 4Å: Chain A: Y.274, L.275, T.276, S.279, Q.283, A.286, A.287, Q.290 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.274 Hydrogen bonds: A:Q.283 MRD.20: 14 residues within 4Å: Chain A: N.111, N.112, A.113, F.130, L.133, V.139, H.142, E.143, I.188, L.202, R.203 Ligands: ZN.5, ZN.6, ZN.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.113, A:F.130, A:L.133, A:V.139, A:I.188, A:L.202 Hydrogen bonds: A:A.113, A:E.143 Water bridges: A:H.231, A:H.231

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

XYP.16: 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:N.159, A:E.160, A:E.160, A:Y.217, A:N.233 Water bridges: A:R.220, A:R.220, A:T.222, A:G.223 Salt bridges: A:R.220 XYP.17: 3 residues within 4Å: Chain A: W.186, S.206, Y.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.206 Water bridges: A:S.204, A:S.206, A:S.206, A:Y.242 XYP.18: 4 residues within 4Å: Chain A: H.216, S.218, K.219, Y.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.218 Salt bridges: A:H.216 XYP.19: 7 residues within 4Å: Chain A: Y.83, V.87, L.175, F.178, Y.179, R.260, D.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.175, A:Y.179, A:R.260, A:R.260, A:D.261 Water bridges: A:D.261

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.21: 4 residues within 4Å: Chain A: Y.211, G.212, D.213, I.232 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.213 MPD.22: 3 residues within 4Å: Chain A: D.94, N.96, Y.151 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.151 Hydrogen bonds: A:D.94, A:D.94, A:D.94, A:N.96

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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