SMTL ID : 6e2v.1

MDDEF in complex with MVAPP, ADPBeF3 and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: A.128, S.130, S.164, S.215 Ligands: DP6.3, BEF.4, ADP.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.130, H2O.2 MG.2: 5 residues within 4Å: Chain A: A.128, S.164, R.167 Ligands: DP6.3, BEF.4 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain B: A.128, S.130, S.164, S.215 Ligands: DP6.8, BEF.9, ADP.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.130, H2O.7 MG.7: 5 residues within 4Å: Chain B: A.128, S.164, R.167 Ligands: DP6.8, BEF.9 No protein-ligand interaction detected (PLIP)

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

DP6.3: 21 residues within 4Å: Chain A: A.37, K.40, Y.41, W.42, K.44, I.50, S.130, S.162, G.163, S.164, R.167, S.215, R.216, M.219, M.266, D.306, A.307 Ligands: MG.1, MG.2, BEF.4, ADP.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:K.40, A:D.306 Hydrogen bonds: A:Y.41, A:Y.41, A:S.130, A:S.162, A:G.163, A:S.164, A:S.164, A:S.215 Water bridges: A:R.167, A:R.167, A:R.216, A:R.216 Salt bridges: A:K.44, A:R.167, A:R.216 DP6.8: 21 residues within 4Å: Chain B: A.37, K.40, Y.41, W.42, K.44, I.50, S.130, S.162, G.163, S.164, R.167, S.215, R.216, M.219, M.266, D.306, A.307 Ligands: MG.6, MG.7, BEF.9, ADP.10 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.40, B:D.306 Hydrogen bonds: B:Y.41, B:Y.41, B:S.130, B:S.162, B:G.163, B:S.164, B:S.164, B:S.215 Water bridges: B:R.167, B:R.167, B:R.216, B:R.216 Salt bridges: B:K.44, B:R.167, B:R.216

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.4: 11 residues within 4Å: Chain A: G.126, L.127, A.128, K.211, S.215, D.306, A.307 Ligands: MG.1, MG.2, DP6.3, ADP.5 No protein-ligand interaction detected (PLIP) BEF.9: 11 residues within 4Å: Chain B: G.126, L.127, A.128, K.211, S.215, D.306, A.307 Ligands: MG.6, MG.7, DP6.8, ADP.10 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 26 residues within 4Å: Chain A: T.66, T.68, F.81, L.83, K.95, V.96, S.117, N.119, T.123, A.124, A.125, G.126, L.127, A.128, S.129, S.130, A.131, G.133, L.134, L.137, K.211, S.214, S.215 Ligands: MG.1, DP6.3, BEF.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.117, A:N.119, A:A.124, A:A.125, A:G.126, A:L.127, A:A.128, A:S.129, A:S.129, A:S.130, A:S.130, A:S.215, A:S.215, A:S.215 Water bridges: A:T.68, A:K.95, A:K.95, A:K.95, A:K.95, A:S.129, A:A.131, A:S.162, A:R.216 Salt bridges: A:K.211, A:K.211 ADP.10: 26 residues within 4Å: Chain B: T.66, T.68, F.81, L.83, K.95, V.96, S.117, N.119, T.123, A.124, A.125, G.126, L.127, A.128, S.129, S.130, A.131, G.133, L.134, L.137, K.211, S.214, S.215 Ligands: MG.6, DP6.8, BEF.9 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:S.117, B:N.119, B:A.124, B:A.125, B:G.126, B:L.127, B:A.128, B:S.129, B:S.129, B:S.130, B:S.130, B:S.215, B:S.215, B:S.215 Water bridges: B:T.68, B:K.95, B:K.95, B:K.95, B:K.95, B:S.129, B:A.131, B:S.162, B:R.216 Salt bridges: B:K.211, B:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C.L. et al., Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase. Nat Commun (2020)

Release Date

2020-01-15

Peptides

Mevalonate diphosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mevalonate diphosphate decarboxylase

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