SMTL ID : 6mde.1

Mevalonate kinase from Methanosarcina mazei with mevalonate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MEV: (R)-MEVALONATE(Non-covalent)

MEV.1: 5 residues within 4Å: Chain A: Y.13, E.17, H.18, G.260, A.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.13 Hydrogen bonds: A:H.18 Water bridges: A:A.261 MEV.10: 6 residues within 4Å: Chain B: Y.13, E.17, H.18, G.93, G.260, A.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.13, B:H.18 Water bridges: B:D.140

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: H.61, P.62, Y.63, V.64 No protein-ligand interaction detected (PLIP) K.11: 7 residues within 4Å: Chain B: P.89, V.90, G.91, L.94, G.95, S.96 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:P.89, B:S.96

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.74, F.114, L.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.74 Water bridges: A:S.74, A:S.74 GOL.4: 5 residues within 4Å: Chain A: Y.142, F.146, G.147, G.148, K.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.142, A:G.147, A:K.157 GOL.5: 4 residues within 4Å: Chain A: S.5, R.36, R.38, D.85 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.5, A:S.5, A:R.36, A:D.85 Water bridges: A:R.38 GOL.6: 2 residues within 4Å: Chain A: D.57, K.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:K.60 GOL.7: 5 residues within 4Å: Chain A: L.41, N.42, N.78, G.79, F.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.42, A:N.42, A:N.78, A:G.79 Water bridges: A:N.78 GOL.8: 8 residues within 4Å: Chain A: G.106, N.109, E.110, L.116, L.118, I.121, L.300, V.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.106, A:N.109 GOL.9: 8 residues within 4Å: Chain A: P.89, V.90, G.91, S.92, L.94, G.95, S.96, S.97 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.89, A:S.92, A:L.94, A:G.95, A:S.96, A:S.97 Water bridges: A:A.98, A:D.140 GOL.12: 5 residues within 4Å: Chain B: G.215, D.216, Y.217, A.218, F.254 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.216, B:D.216, B:Y.217, B:A.218 Water bridges: B:G.215 GOL.13: 9 residues within 4Å: Chain B: V.90, G.91, G.93, L.94, G.95, S.96, S.97, D.140 Ligands: K.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.91, B:G.95, B:S.96, B:S.96, B:S.97, B:D.140, B:D.140 Water bridges: B:G.93, B:S.97 GOL.14: 6 residues within 4Å: Chain B: V.90, D.169, G.171, V.172, F.173, G.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.171, B:G.265 GOL.15: 3 residues within 4Å: Chain B: F.58, A.66, K.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.131 GOL.16: 1 residues within 4Å: Chain B: D.162 No protein-ligand interaction detected (PLIP) GOL.17: 6 residues within 4Å: Chain B: S.92, G.93, S.174, T.176, A.261, G.262 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.92, B:G.93, B:S.174, B:S.174, B:G.262 Water bridges: B:C.266 GOL.18: 2 residues within 4Å: Chain B: V.172, E.240 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, B.R. et al., Structural insight into substrate and product binding in an archaeal mevalonate kinase. PLoS ONE (2018)

Release Date

2018-12-19

Peptides

Mevalonate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mevalonate kinase

Related Entries With Identical Sequence