SMTL ID : 6mdf.1

Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

2 x PMV: (3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID(Non-covalent)

PMV.1: 12 residues within 4Å: Chain A: K.11, Y.13, E.17, H.18, V.21, S.92, G.93, D.140, T.176, V.180, G.260, A.261 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.13, A:T.176, A:V.180, A:A.261 Hydrogen bonds: A:H.18, A:S.92, A:T.176 Salt bridges: A:K.11 PMV.9: 11 residues within 4Å: Chain B: Y.13, E.17, H.18, V.20, V.21, G.93, D.140, V.180, G.260, A.261 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.18, B:G.93 Salt bridges: B:H.18

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.222, N.225, Y.246, R.249 Chain B: D.232, G.235 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.222, A:R.222, A:R.222, A:N.225, A:R.249, B:D.232 Water bridges: A:Y.246, B:G.235 GOL.3: 2 residues within 4Å: Chain A: H.126, P.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.126 GOL.4: 8 residues within 4Å: Chain A: L.118, T.145, F.146, E.297, Q.298, G.299, L.300, K.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.298, A:G.299, A:L.300 Water bridges: A:F.146, A:E.297 GOL.5: 2 residues within 4Å: Chain A: E.32, K.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.294, A:K.294 GOL.6: 6 residues within 4Å: Chain A: G.23, E.24, T.25, P.153, E.154, R.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:R.206 GOL.7: 3 residues within 4Å: Chain A: F.114, G.115, L.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.115 Water bridges: A:F.114 GOL.8: 6 residues within 4Å: Chain A: D.162, C.163, G.164, P.273, C.276, K.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.162, A:D.162 GOL.10: 4 residues within 4Å: Chain A: D.232, G.235 Chain B: N.225, R.249 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.232, B:N.225 Water bridges: A:G.235, A:G.235, B:R.249 GOL.11: 6 residues within 4Å: Chain B: K.60, H.61, P.62, Y.63, V.64, V.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.61, B:Y.63, B:V.64 GOL.12: 5 residues within 4Å: Chain B: V.90, D.169, G.171, V.172, G.265 4 PLIP interactions: 4 interactions with chain B Water bridges: B:V.90, B:V.90, B:K.289, B:K.289 GOL.13: 7 residues within 4Å: Chain B: G.91, G.93, L.94, G.95, S.96, S.97 Ligands: PMV.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.91, B:G.95, B:S.96 Water bridges: B:L.94, B:L.94 GOL.14: 4 residues within 4Å: Chain B: S.247, A.282, G.285, A.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.285 GOL.15: 1 residues within 4Å: Chain B: 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

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