SMTL ID : 5uuc.1

Tetragonal thermolysin cryocooled to 100 K with 50% 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.138, A:E.177, A:D.185, A:E.190, H2O.4 CA.3: 4 residues within 4Å: Chain A: D.57, D.59, Q.61, F.62 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.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.4, H2O.11

9 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.9 ZN.6: 6 residues within 4Å: Chain A: Y.157, E.166, H.231 Ligands: ZN.5, ZN.7, MRD.20 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.231, H2O.1, H2O.4, H2O.8, H2O.9 ZN.7: 5 residues within 4Å: Chain A: E.143, H.146 Ligands: ZN.5, ZN.6, MRD.20 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.143, H2O.2, H2O.4, H2O.8, H2O.9 ZN.8: 3 residues within 4Å: Chain A: D.226, V.230, H.231 2 PLIP interactions: 2 interactions with chain A Metal complexes: 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.13, CL.14, CL.15 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.15, CL.16 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, H2O.9 ZN.11: 3 residues within 4Å: Chain A: L.202, Y.211 Ligands: ZN.12 No protein-ligand interaction detected (PLIP) ZN.12: 3 residues within 4Å: Chain A: R.203, D.213 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:D.213, H2O.2, H2O.6

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

CL.13: 8 residues within 4Å: Chain A: K.239, Y.242, L.243, G.247, G.248, T.249 Ligands: ZN.9, CL.14 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: S.206, K.239 Ligands: ZN.9, CL.13 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain A: D.207, D.215, K.239, H.250 Ligands: ZN.9, ZN.10, CL.16 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: T.249, H.250, Y.251 Ligands: ZN.10, CL.15 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: R.285, V.289, K.307 Ligand excluded by PLIP

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

MPD.18: 8 residues within 4Å: Chain A: Y.274, L.275, T.276, S.279, Q.283, A.286, A.287, Q.290 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.274, A:A.287, A:Q.290 Hydrogen bonds: A:A.287 MPD.19: 7 residues within 4Å: Chain A: Q.31, D.32, N.33, G.36, N.37, G.38, F.40 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.40 MPD.21: 5 residues within 4Å: Chain A: I.1, S.25, T.26, Y.27, Y.29 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.27 MPD.22: 4 residues within 4Å: Chain A: D.94, N.96, Y.151 Ligands: MRD.23 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.96

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

MRD.20: 15 residues within 4Å: Chain A: N.111, N.112, A.113, F.130, L.133, V.139, H.142, E.143, D.170, I.188, L.202, R.203 Ligands: ZN.5, ZN.6, ZN.7 13 PLIP interactions: 13 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:N.112, A:E.143, A:R.203 Water bridges: A:R.203, A:H.231, A:H.231, A:H.231 MRD.23: 5 residues within 4Å: Chain A: L.91, G.95, N.96, N.97 Ligands: MPD.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.91, 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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