SMTL ID : 6n10.1

Crystal structure of Arabidopsis thaliana mevalonate 5-diphosphate decarboxylase 1 complexed with (R)-MVAPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x DP6: (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID(Non-covalent)

DP6.1: 19 residues within 4Å: Chain A: A.22, K.25, Y.26, W.27, K.29, I.35, S.41, R.81, S.132, S.164, G.165, S.166, R.169, S.219, T.220, M.223, F.271, D.313, A.314 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.27, A:F.271 Hydrogen bonds: A:Y.26, A:Y.26, A:S.132, A:S.164, A:S.164, A:G.165, A:S.166, A:S.166, A:S.219, A:T.220 Water bridges: A:R.81, A:G.163, A:R.169 Salt bridges: A:K.29, A:R.81, A:R.169 DP6.6: 19 residues within 4Å: Chain B: A.22, K.25, Y.26, W.27, K.29, I.35, S.41, R.81, S.132, S.164, G.165, S.166, R.169, S.219, T.220, M.223, F.271, D.313, A.314 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.27, B:F.271 Hydrogen bonds: B:Y.26, B:Y.26, B:S.132, B:S.164, B:S.164, B:G.165, B:S.166, B:S.166, B:S.219, B:T.220 Water bridges: B:R.81, B:G.163, B:R.169 Salt bridges: B:K.29, B:R.81, B:R.169

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: S.62, F.63, D.64, R.65, R.67, H.116, L.413 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.64, A:D.64, A:R.65 Salt bridges: A:R.65, A:R.67, A:H.116 SO4.3: 6 residues within 4Å: Chain A: F.172, G.173, Q.193, D.196, R.394, G.395 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.173, A:Q.193, A:G.395 Water bridges: A:R.394, A:R.394 SO4.4: 3 residues within 4Å: Chain A: L.399, Q.400, D.401 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.400, A:D.401 SO4.5: 3 residues within 4Å: Chain A: K.183, E.184, D.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.184 SO4.7: 7 residues within 4Å: Chain B: S.62, F.63, D.64, R.65, R.67, H.116, L.413 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.64, B:D.64, B:D.64, B:R.65 Salt bridges: B:R.65, B:R.67, B:H.116 SO4.8: 6 residues within 4Å: Chain B: F.172, G.173, Q.193, D.196, R.394, G.395 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.173, B:Q.193, B:G.395 Water bridges: B:R.394, B:R.394 SO4.9: 3 residues within 4Å: Chain B: L.399, Q.400, D.401 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.400, B:D.401 SO4.10: 3 residues within 4Å: Chain B: K.183, E.184, D.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, S.T. et al., Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase. Acs Chem.Biol. (2019)

Release Date

2019-07-17

Peptides

Diphosphomevalonate decarboxylase MVD1, peroxisomal: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diphosphomevalonate decarboxylase MVD1, peroxisomal