SMTL ID : 7yst.1

Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-glucose and UDP-galactose in chain B from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.7, A.9, G.10, F.11, I.12, D.31, N.32, F.33, A.34, T.35, G.36, A.55, D.56, I.57, L.77, A.78, A.79, I.81, V.96, T.119, S.120, Y.146, K.150, P.173, A.174, N.175, V.176 Ligands: UPG.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.173, A:V.176 Hydrogen bonds: A:A.9, A:F.11, A:I.12, A:N.32, A:F.33, A:A.34, A:T.35, A:T.35, A:T.35, A:G.36, A:D.56, A:I.57, A:L.77, A:A.79, A:K.150, A:V.176, A:V.176, A:Q.181 Water bridges: A:G.10, A:G.13, A:N.32, A:N.32, A:T.35, A:I.81 NAD.5: 29 residues within 4Å: Chain B: G.7, A.9, G.10, F.11, I.12, D.31, N.32, F.33, A.34, T.35, G.36, A.55, D.56, I.57, L.77, A.78, A.79, I.81, V.96, T.119, S.120, Y.146, K.150, P.173, A.174, N.175, V.176 Ligands: UPG.7, GDU.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.173, B:V.176 Hydrogen bonds: B:G.7, B:F.11, B:I.12, B:N.32, B:N.32, B:F.33, B:A.34, B:T.35, B:T.35, B:T.35, B:G.36, B:D.56, B:I.57, B:L.77, B:A.79, B:K.150, B:V.176, B:V.176, B:Q.181 Water bridges: B:G.10, B:G.13, B:T.35

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

EDO.2: 5 residues within 4Å: Chain A: T.242, K.244, P.293, I.295, E.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.244, A:P.293 Water bridges: A:I.295 EDO.3: 3 residues within 4Å: Chain A: F.267, H.268, P.269 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.267, A:H.268, A:H.268 EDO.6: 3 residues within 4Å: Chain B: R.161, H.162, G.165 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.161, B:H.162, B:G.165

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

UPG.4: 24 residues within 4Å: Chain A: I.81, R.84, S.121, G.122, G.123, Y.146, P.173, A.174, N.175, E.186, A.187, G.188, V.189, I.192, F.193, R.204, V.205, F.206, N.211, R.213, Y.215, D.248, R.271 Ligands: NAD.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.189 Hydrogen bonds: A:I.81, A:G.123, A:Y.146, A:Y.146, A:P.173, A:N.175, A:G.188, A:V.189, A:R.204 Water bridges: A:R.84, A:R.84, A:R.84, A:V.176, A:N.211, A:R.213, A:Y.215, A:D.274, A:D.274 Salt bridges: A:R.84, A:R.84, A:R.213, A:R.271 pi-Stacking: A:F.206 UPG.7: 24 residues within 4Å: Chain B: I.81, R.84, S.121, G.123, Y.146, P.173, A.174, N.175, A.187, G.188, V.189, I.192, F.193, R.204, V.205, F.206, N.211, R.213, Y.215, D.248, R.271, D.274 Ligands: NAD.5, GDU.8 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.192 Hydrogen bonds: B:I.81, B:G.123, B:S.124, B:Y.146, B:P.173, B:N.175, B:G.188, B:V.189, B:R.204, B:R.271 Water bridges: B:R.84, B:R.84, B:R.84, B:V.176, B:R.204, B:N.211, B:R.213, B:R.271 Salt bridges: B:R.84, B:R.84, B:R.213 pi-Stacking: B:F.206

1 x GDU: GALACTOSE-URIDINE-5'-DIPHOSPHATE(Non-covalent)

GDU.8: 22 residues within 4Å: Chain B: I.81, V.83, R.84, S.121, S.124, Y.146, N.175, A.187, G.188, V.189, I.192, F.193, R.204, V.205, F.206, N.211, R.213, Y.215, D.248, R.271 Ligands: NAD.5, UPG.7 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.192 Hydrogen bonds: B:S.121, B:S.121, B:Y.146, B:N.175, B:G.188, B:V.189, B:R.204, B:F.206, B:R.271, B:D.274 Water bridges: B:R.84, B:R.84, B:R.84, B:G.123, B:Q.181, B:Q.181, B:R.204, B:N.211, B:R.213, B:R.271 Salt bridges: B:R.84, B:R.84, B:R.213 pi-Stacking: B:F.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, S. et al., Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-glucose and UDP-galactose in chain B from Mycobacterium tuberculosis. To Be Published

Release Date

2023-08-16

Peptides

UDP-glucose 4-epimerase along with EC 5.1.3.2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-glucose 4-epimerase along with EC 5.1.3.2

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