SMTL ID : 3mve.1

Crystal structure of a novel pyruvate decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: H.79, S.80, H.94 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.80, A:S.80 Water bridges: A:H.79, A:H.79 Salt bridges: A:H.79, A:H.94, B:K.162 SO4.10: 3 residues within 4Å: Chain B: H.79, S.80, H.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.80, B:S.80 Salt bridges: B:H.79, B:H.94 SO4.11: 7 residues within 4Å: Chain B: G.201, L.202, D.203, F.271, R.272, F.273, G.274 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.202, B:D.203, B:D.203, B:F.273, B:G.274 SO4.12: 3 residues within 4Å: Chain B: G.178, K.179, K.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.179 Salt bridges: B:K.237 SO4.13: 7 residues within 4Å: Chain B: H.216, L.217, H.220, I.222, I.406, K.407, E.410 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.216, B:K.407, B:E.410 Salt bridges: B:H.220

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: G.201, L.202, R.272, F.273, P.298, Y.316, V.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.202, A:R.272, A:F.273, A:Y.316 EDO.3: 8 residues within 4Å: Chain A: Y.93, T.103, M.107 Chain B: Q.110, L.152, S.155, E.159 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.110, B:S.155, B:E.159 EDO.4: 8 residues within 4Å: Chain A: Y.93, T.103, L.145, Q.148, A.149, L.152 Chain B: S.155 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.93, A:T.103, A:L.145 EDO.5: 6 residues within 4Å: Chain A: L.125, E.159, K.162, K.163 Chain B: G.92, Y.93 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.93, A:E.159, A:E.159, A:K.163 EDO.6: 3 residues within 4Å: Chain A: F.46, S.47, W.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.47, A:W.48 EDO.7: 5 residues within 4Å: Chain A: F.283, G.347, F.348, S.351, R.352 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.347, A:S.351, A:R.352 Water bridges: A:Q.286 EDO.8: 5 residues within 4Å: Chain A: S.77, K.78, H.79, S.95, G.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.78, A:S.95 EDO.9: 8 residues within 4Å: Chain A: K.21, E.22, T.23, R.50, N.97, W.98, A.99, L.145 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.21, A:T.23, A:T.23, A:R.50, A:N.97, A:W.98, A:A.99 Water bridges: A:E.22, A:R.50, A:A.146 EDO.14: 8 residues within 4Å: Chain B: K.21, E.22, T.23, R.50, N.97, W.98, A.99, L.145 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.21, B:T.23, B:T.23, B:R.50, B:N.97, B:A.99 Water bridges: B:E.22, B:W.98, B:A.146 EDO.15: 6 residues within 4Å: Chain B: V.58, G.61, V.62, D.63, P.64, R.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.58, B:R.211, B:R.211 Water bridges: B:D.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.J. et al., FrsA functions as a cofactor-independent decarboxylase to control metabolic flux. Nat.Chem.Biol. (2011)

Release Date

2011-05-18

Peptides

UPF0255 protein VV1_0328: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UPF0255 protein VV1_0328

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