SMTL ID : 6vlo.1 (1 other biounit)

X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 14 residues within 4Å: Chain A: N.181, E.190, K.191, L.192, K.195, F.196, H.207, I.208, Q.209, S.214, R.216, V.251, R.276, R.282 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:K.195 Hydrogen bonds: A:N.181, A:L.192, A:K.195, A:H.207, A:Q.209, A:S.214, A:S.214, A:R.216 Water bridges: A:I.193, A:R.276, A:R.282, A:R.282, A:R.282, A:R.282 Salt bridges: A:K.191, A:K.191, A:R.216, A:R.276, A:R.276, A:R.282 TYD.3: 14 residues within 4Å: Chain B: N.181, E.190, K.191, L.192, K.195, F.196, H.207, I.208, Q.209, S.214, R.216, V.251, R.276, R.282 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.181, B:N.181, B:L.192, B:H.207, B:Q.209, B:Q.209, B:S.214, B:R.216, B:R.216 Water bridges: B:I.193, B:S.214, B:R.282, B:R.282 Salt bridges: B:K.191, B:K.191, B:R.216, B:R.276, B:R.276, B:R.282

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 24 residues within 4Å: Chain A: G.11, L.13, G.14, F.15, I.16, G.17, D.37, I.38, G.39, D.40, C.42, A.43, G.59, D.60, I.61, F.82, A.83, A.84, S.86, T.101, M.125, S.126, T.127, K.156 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.11, A:F.15, A:I.16, A:G.17, A:I.38, A:G.39, A:D.40, A:D.40, A:I.61, A:F.82, A:A.84, A:S.86, A:T.101, A:S.126, A:K.156, A:K.156 Water bridges: A:C.42, A:M.125 NAD.4: 27 residues within 4Å: Chain B: G.11, L.13, G.14, F.15, I.16, D.37, I.38, G.39, D.40, C.42, A.43, G.59, D.60, I.61, F.82, A.83, A.84, S.86, T.101, M.125, S.126, T.127, K.156, C.179, N.180, N.181, V.182 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.16, B:T.127, B:V.182 Hydrogen bonds: B:G.11, B:F.15, B:I.16, B:G.17, B:I.38, B:G.39, B:D.40, B:D.40, B:D.60, B:I.61, B:F.82, B:A.84, B:S.86, B:K.156, B:K.156, B:V.182 Water bridges: B:G.14, B:M.125, B:V.182, B:Q.187, B:Q.187

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 2 residues within 4Å: Chain B: H.69, H.74 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.69, B:H.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferek, J.D. et al., Biochemical analysis of a sugar 4,6-dehydratase from Acanthamoeba polyphaga Mimivirus. Protein Sci. (2020)

Release Date

2020-03-04

Peptides

Putative dTDP-D-glucose 4,6-dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative dTDP-D-glucose 4,6-dehydratase

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