SMTL ID : 6e2y.1

MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 11 residues within 4Å: Chain A: G.126, L.127, A.128, K.211, S.215, D.306, A.307 Ligands: ADP.2, DP6.3, CO.4, CO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.126, A:A.128, A:S.215, A:S.215, A:A.307 Salt bridges: A:K.211 SO4.6: 11 residues within 4Å: Chain B: G.126, L.127, A.128, K.211, S.215, D.306, A.307 Ligands: ADP.7, DP6.8, CO.9, CO.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.126, B:A.128, B:S.215, B:S.215, B:A.307 Salt bridges: B:K.211

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

ADP.2: 25 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, G.133, L.134, L.137, K.211, S.214, S.215 Ligands: SO4.1, DP6.3, CO.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.119, 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.215, A:S.215 Water bridges: A:T.68, A:S.129, A:A.131, A:S.162, A:R.216 Salt bridges: A:K.211, A:K.211 ADP.7: 25 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, G.133, L.134, L.137, K.211, S.214, S.215 Ligands: SO4.6, DP6.8, CO.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.119, 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.215, B:S.215 Water bridges: B:T.68, B:S.129, B:A.131, B:S.162, B:R.216 Salt bridges: B:K.211, B:K.211

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

DP6.3: 22 residues within 4Å: Chain A: A.37, K.40, Y.41, W.42, K.44, I.50, S.56, S.130, S.162, G.163, S.164, R.167, S.215, R.216, M.219, M.266, D.306, A.307 Ligands: SO4.1, ADP.2, CO.4, CO.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.37, A:W.42 Hydrogen bonds: A:Y.41, A:Y.41, A:Y.41, A:S.162, A:S.162, A:G.163, A:S.164, A:S.164, A:S.215, A:A.307 Water bridges: A:R.167, A:R.216, A:R.216 Salt bridges: A:K.44, A:R.167, A:R.216 DP6.8: 22 residues within 4Å: Chain B: A.37, K.40, Y.41, W.42, K.44, I.50, S.56, S.130, S.162, G.163, S.164, R.167, S.215, R.216, M.219, M.266, D.306, A.307 Ligands: SO4.6, ADP.7, CO.9, CO.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.37, B:W.42 Hydrogen bonds: B:Y.41, B:Y.41, B:Y.41, B:S.162, B:S.162, B:G.163, B:S.164, B:S.164, B:S.215, B:A.307 Water bridges: B:R.167, B:R.216, B:R.216 Salt bridges: B:K.44, B:R.167, B:R.216

4 x CO: COBALT (II) ION(Non-covalent)

CO.4: 7 residues within 4Å: Chain A: A.128, S.130, S.164, S.215 Ligands: SO4.1, ADP.2, DP6.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.130, H2O.1 CO.5: 6 residues within 4Å: Chain A: A.37, A.128, R.167, D.306 Ligands: SO4.1, DP6.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.306, H2O.2 CO.9: 7 residues within 4Å: Chain B: A.128, S.130, S.164, S.215 Ligands: SO4.6, ADP.7, DP6.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.130, H2O.7 CO.10: 6 residues within 4Å: Chain B: A.37, A.128, R.167, D.306 Ligands: SO4.6, DP6.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.306, H2O.7

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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