SMTL ID : 6dnt.1

UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with UDP-N-acetylmuramic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.43, L.45, G.46, F.47, I.48, D.66, N.67, L.68, S.69, S.70, G.71, E.89, D.90, L.91, L.109, A.110, A.111, A.113, N.128, S.151, S.152, S.153, Y.177, K.181, Y.204, F.205, V.207 Ligands: EPZ.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.204 Hydrogen bonds: A:L.45, A:F.47, A:I.48, A:N.67, A:N.67, A:L.68, A:S.69, A:S.69, A:S.70, A:S.70, A:S.70, A:S.70, A:G.71, A:L.91, A:L.109, A:A.111, A:N.128, A:S.151, A:K.181, A:V.207 Water bridges: A:G.46, A:G.49, A:Q.212, A:Q.212 pi-Stacking: A:Y.204 NAD.8: 28 residues within 4Å: Chain B: G.43, L.45, G.46, F.47, I.48, D.66, N.67, L.68, S.69, S.70, G.71, E.89, D.90, L.91, L.109, A.110, A.111, A.113, N.128, S.151, S.152, S.153, Y.177, K.181, Y.204, F.205, V.207 Ligands: EPZ.9 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.204 Hydrogen bonds: B:L.45, B:F.47, B:I.48, B:N.67, B:N.67, B:L.68, B:S.69, B:S.69, B:S.70, B:S.70, B:S.70, B:S.70, B:G.71, B:L.91, B:L.109, B:A.111, B:N.128, B:S.151, B:Y.177, B:K.181, B:V.207 Water bridges: B:G.46, B:G.49, B:Q.212, B:Q.212 pi-Stacking: B:Y.204

2 x EPZ: (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid(Non-covalent)

EPZ.2: 22 residues within 4Å: Chain A: A.113, S.153, S.154, A.155, Y.177, Y.204, F.205, N.206, Q.212, Y.218, A.220, V.221, K.224, V.236, I.237, Y.238, Q.243, R.245, I.279, R.302, D.305 Ligands: NAD.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.220, A:V.221, A:K.224, A:Y.238 Hydrogen bonds: A:S.153, A:S.153, A:S.154, A:Y.177, A:N.206, A:Q.212, A:V.221, A:K.224, A:V.236, A:Y.238, A:Q.243, A:R.302 Water bridges: A:V.207, A:Y.218, A:R.245, A:R.245, A:R.245, A:R.302, A:R.302, A:D.305, A:D.305 Salt bridges: A:R.245, A:R.302 EPZ.9: 22 residues within 4Å: Chain B: A.113, S.153, S.154, A.155, Y.177, Y.204, F.205, N.206, Q.212, Y.218, A.220, V.221, K.224, V.236, I.237, Y.238, Q.243, R.245, I.279, R.302, D.305 Ligands: NAD.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.220, B:V.221, B:K.224, B:Y.238 Hydrogen bonds: B:S.153, B:S.153, B:S.154, B:N.206, B:Q.212, B:V.221, B:K.224, B:V.236, B:Y.238, B:Q.243, B:R.302 Water bridges: B:V.207, B:Y.218, B:R.245, B:R.245, B:R.245, B:R.245, B:R.302, B:R.302 Salt bridges: B:R.245, B:R.302

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: E.242, H.308 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.242, A:E.242, A:H.308 ZN.10: 2 residues within 4Å: Chain B: E.242, H.308 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.242, B:E.242, B:H.308

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

EDO.4: 5 residues within 4Å: Chain A: S.70, L.112, A.113, S.114, Y.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:Y.125 Water bridges: A:A.113, A:R.124 EDO.5: 6 residues within 4Å: Chain A: N.280, F.283, E.284, D.295, V.296, Y.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.284, A:D.295 EDO.6: 2 residues within 4Å: Chain A: E.301, K.307 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.301 EDO.7: 2 residues within 4Å: Chain A: D.90, D.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.90 EDO.11: 5 residues within 4Å: Chain B: S.70, L.112, A.113, S.114, Y.125 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.70, B:S.70, B:Y.125 Water bridges: B:A.113, B:R.124 EDO.12: 6 residues within 4Å: Chain B: N.280, F.283, E.284, D.295, V.296, Y.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.284, B:E.284, B:D.295 EDO.13: 2 residues within 4Å: Chain B: E.301, K.307 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.301 EDO.14: 2 residues within 4Å: Chain B: D.90, D.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carbone, V. et al., Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid. Proteins (2018)

Release Date

2018-10-03

Peptides

NAD-dependent epimerase/dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD-dependent epimerase/dehydratase