SMTL ID : 6pnl.1

Structure of Epimerase Mth375 from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: G.54, A.56, G.57, C.58, V.59, D.78, N.79, L.80, S.81, S.82, S.83, G.99, D.100, I.101, L.121, A.122, A.123, F.125, V.140, S.163, S.164, S.165, Y.191, K.195, F.218, N.220, V.221, R.232, N.233 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.218 Hydrogen bonds: A:G.54, A:C.58, A:V.59, A:N.79, A:N.79, A:S.81, A:S.81, A:S.82, A:S.82, A:S.82, A:S.82, A:S.83, A:D.100, A:I.101, A:L.121, A:A.123, A:S.163, A:V.221, A:N.233 Water bridges: A:G.57, A:G.60, A:K.195, A:V.221, A:E.226 Salt bridges: A:R.232, A:R.232 NAD.7: 29 residues within 4Å: Chain B: G.54, A.56, G.57, C.58, V.59, D.78, N.79, L.80, S.81, S.82, S.83, G.99, D.100, I.101, L.121, A.122, A.123, F.125, V.140, S.163, S.164, S.165, Y.191, K.195, F.218, N.220, V.221, R.232, N.233 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:F.218 Hydrogen bonds: B:G.54, B:C.58, B:V.59, B:N.79, B:N.79, B:S.81, B:S.81, B:S.82, B:S.82, B:S.82, B:S.82, B:S.83, B:D.100, B:I.101, B:L.121, B:A.123, B:S.163, B:Y.191, B:V.221, B:N.233 Water bridges: B:G.57, B:G.60, B:K.195, B:V.221, B:E.226 Salt bridges: B:R.232, B:R.232

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 15 residues within 4Å: Chain A: N.127, C.167, N.220, N.233, V.234, F.238, W.241, P.249, I.250, T.251, E.256, R.258, V.294, R.317, D.320 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.234 Hydrogen bonds: A:N.127, A:N.220, A:V.234, A:P.249, A:T.251, A:T.251, A:T.251, A:R.317 Water bridges: A:R.258, A:R.258, A:R.317, A:R.317 Salt bridges: A:R.258, A:R.317, A:R.317 UDP.8: 15 residues within 4Å: Chain B: N.127, C.167, N.220, N.233, V.234, F.238, W.241, P.249, I.250, T.251, E.256, R.258, V.294, R.317, D.320 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.234 Hydrogen bonds: B:N.127, B:N.220, B:V.234, B:P.249, B:T.251, B:T.251, B:R.317 Water bridges: B:R.258, B:R.258, B:R.317, B:R.317 Salt bridges: B:R.258, B:R.317, B:R.317

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

EDO.3: 4 residues within 4Å: Chain A: D.103, D.104, E.105, K.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.108, A:K.108 Water bridges: A:D.104, A:D.104 EDO.4: 6 residues within 4Å: Chain A: S.61, N.62, N.87, P.224, G.225, W.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.61 EDO.5: 4 residues within 4Å: Chain A: E.179, E.180, H.181, K.331 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.180, A:H.181 Water bridges: A:E.180, A:K.331, A:R.334 EDO.9: 4 residues within 4Å: Chain B: D.103, D.104, E.105, K.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.108, B:K.108 Water bridges: B:D.104 EDO.10: 6 residues within 4Å: Chain B: S.61, N.62, N.87, P.224, G.225, W.354 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61 EDO.11: 4 residues within 4Å: Chain B: E.179, E.180, H.181, K.331 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.180, B:H.181 Water bridges: B:E.180, B:K.331, B:R.334

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

SO4.6: 4 residues within 4Å: Chain A: T.290, H.292, S.343, F.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.290, A:F.344 Water bridges: A:S.343 Salt bridges: A:H.292 SO4.12: 4 residues within 4Å: Chain B: T.290, H.292, S.343, F.344 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.344 Water bridges: B:S.343 Salt bridges: B:H.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carbone, V. et al., Structure of a UDP-GALE 4-epimerase (Mth375) from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus. To Be Published

Release Date

2020-07-08

Peptides

UDP-glucose 4-epimerase related protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-glucose 4-epimerase related protein

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