SMTL ID : 6qar.1

Thermolysine under 2 kbar of argon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.115, H.146, D.150, Y.157, N.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:W.115, A:W.115, A:L.155

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

DMS.2: 3 residues within 4Å: Chain A: H.216, S.218, Y.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.218 pi-Cation interactions: A:H.216

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.4 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.4: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.1, H2O.4 CA.5: 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.3, H2O.7 CA.6: 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.2

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166 Ligands: CL.31 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166

20 x AR: ARGON(Non-covalent)

AR.8: 4 residues within 4Å: Chain A: Y.84, S.92, Y.93, L.144 No protein-ligand interaction detected (PLIP) AR.9: 8 residues within 4Å: Chain A: R.35, G.36, N.37, G.38, Y.81, S.92, A.98, I.100 No protein-ligand interaction detected (PLIP) AR.10: 5 residues within 4Å: Chain A: E.160, Y.217, R.220, N.233, F.281 No protein-ligand interaction detected (PLIP) AR.11: 3 residues within 4Å: Chain A: D.57, A.58 Ligands: AR.27 No protein-ligand interaction detected (PLIP) AR.12: 3 residues within 4Å: Chain A: Y.27, A.56 Ligands: AR.27 No protein-ligand interaction detected (PLIP) AR.13: 5 residues within 4Å: Chain A: I.131, D.191, V.192, Y.193, P.195 No protein-ligand interaction detected (PLIP) AR.14: 2 residues within 4Å: Chain A: G.259, R.260 No protein-ligand interaction detected (PLIP) AR.15: 4 residues within 4Å: Chain A: T.249, H.250, Y.251, G.252 No protein-ligand interaction detected (PLIP) AR.16: 3 residues within 4Å: Chain A: K.18, N.19, Y.75 No protein-ligand interaction detected (PLIP) AR.17: 4 residues within 4Å: Chain A: Y.81, K.85, L.91, N.97 No protein-ligand interaction detected (PLIP) AR.18: 3 residues within 4Å: Chain A: S.5, N.33, T.34 No protein-ligand interaction detected (PLIP) AR.19: 2 residues within 4Å: Chain A: P.277, T.278 No protein-ligand interaction detected (PLIP) AR.20: 4 residues within 4Å: Chain A: G.252, V.253, S.254, Q.308 No protein-ligand interaction detected (PLIP) AR.21: 2 residues within 4Å: Chain A: K.45, S.53 No protein-ligand interaction detected (PLIP) AR.22: 3 residues within 4Å: Chain A: V.13, A.68, P.132 No protein-ligand interaction detected (PLIP) AR.23: 7 residues within 4Å: Chain A: I.164, I.168, I.171, I.237, F.267, L.284 Ligands: AR.26 No protein-ligand interaction detected (PLIP) AR.24: 1 residues within 4Å: Chain A: Q.301 No protein-ligand interaction detected (PLIP) AR.25: 4 residues within 4Å: Chain A: Y.84, V.148, F.172, L.271 No protein-ligand interaction detected (PLIP) AR.26: 6 residues within 4Å: Chain A: I.168, F.267, A.270, L.275, L.284 Ligands: AR.23 No protein-ligand interaction detected (PLIP) AR.27: 5 residues within 4Å: Chain A: Y.27, A.56, D.57 Ligands: AR.11, AR.12 No protein-ligand interaction detected (PLIP)

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

CL.28: 7 residues within 4Å: Chain A: G.12, V.13, L.14, G.15, D.16, K.18, D.72 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain A: R.285, V.289, K.307 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: Y.75, K.182 Ligand excluded by PLIP CL.31: 7 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: ZN.7, VAL.37 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain A: N.37, A.98, A.99 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain A: Q.225, D.226 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain A: Y.24 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain A: A.64, S.65 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain A: Y.211 Ligand excluded by PLIP

1 x VAL: VALINE(Non-covalent)

VAL.37: 9 residues within 4Å: Chain A: N.112, A.113, L.133, E.143, L.202, R.203, H.231 Ligands: CL.31, LYS.38 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.133, A:L.202 Hydrogen bonds: A:E.143, A:R.203, A:R.203, K.38

1 x LYS: LYSINE(Non-covalent)

LYS.38: 4 residues within 4Å: Chain A: N.111, N.112, H.231 Ligands: VAL.37 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain A Hydrogen bonds: K.38, A:N.112, A:N.112, A:N.112 Water bridges: A:N.111 Salt bridges: A:H.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prange, T. et al., Labelling protein crystals by argon at 2 kbar. To be published

Release Date

2020-01-15

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

Related Entries With Identical Sequence