SMTL ID : 5br7.1 (1 other biounit)

Structure of UDP-galactopyranose mutase from Corynebacterium diphtheriae in complex with citrate ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: V.9, G.10, S.11, G.12, L.13, F.14, V.33, E.34, K.35, R.36, G.41, N.42, Y.58, G.59, A.60, H.61, L.62, T.219, D.220, W.221, F.222, T.240, G.241, P.242, Y.325, Y.326, G.357, R.358, L.359, Y.364, L.365, D.366, M.367, A.370 Ligands: NA.7, FLC.11 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:Y.325, A:Y.364 Hydrogen bonds: A:S.11, A:G.12, A:F.14, A:K.35, A:R.36, A:G.41, A:N.42, A:H.61, A:L.62, A:L.62, A:D.220, A:D.220, A:W.221, A:T.240, A:R.358, A:Y.364, A:M.367 Water bridges: A:L.13, A:G.15, A:G.15, A:N.42, A:N.42, A:A.43, A:R.358, A:R.358, A:L.359, A:H.368 Salt bridges: A:R.358 pi-Stacking: A:H.61 pi-Cation interactions: A:H.61 FAD.12: 36 residues within 4Å: Chain B: V.9, G.10, S.11, G.12, L.13, F.14, V.33, E.34, K.35, R.36, G.41, N.42, Y.58, G.59, A.60, H.61, L.62, T.219, D.220, W.221, F.222, T.240, G.241, P.242, Y.325, Y.326, G.357, R.358, L.359, Y.364, L.365, D.366, M.367, A.370 Ligands: NA.18, FLC.22 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:Y.325, B:Y.364 Hydrogen bonds: B:S.11, B:G.12, B:F.14, B:K.35, B:R.36, B:G.41, B:N.42, B:H.61, B:L.62, B:L.62, B:D.220, B:W.221, B:R.358, B:D.366, B:M.367 Water bridges: B:L.13, B:G.15, B:G.15, B:N.42, B:N.42, B:A.43, B:Y.326, B:R.358, B:R.358, B:L.359, B:H.368 Salt bridges: B:R.358 pi-Stacking: B:H.61 pi-Cation interactions: B:H.61

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

EDO.2: 6 residues within 4Å: Chain A: E.54, H.56, A.60, H.61, Y.200, F.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.54, A:H.61 EDO.3: 4 residues within 4Å: Chain A: E.264, F.271, I.310, K.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.312 Water bridges: A:Y.286 EDO.4: 4 residues within 4Å: Chain A: H.64, D.366, H.368, M.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.366, A:H.368 EDO.5: 1 residues within 4Å: Chain A: Y.314 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.260, A:D.260 EDO.13: 6 residues within 4Å: Chain B: E.54, H.56, A.60, H.61, Y.200, F.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.54, B:H.61 EDO.14: 4 residues within 4Å: Chain B: E.264, F.271, I.310, K.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.312 EDO.15: 4 residues within 4Å: Chain B: H.64, D.366, H.368, M.369 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.368 EDO.16: 1 residues within 4Å: Chain B: Y.314 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.260

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: S.126, I.129, D.130, S.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.126 NA.7: 3 residues within 4Å: Chain A: A.60 Ligands: FAD.1, FLC.11 No protein-ligand interaction detected (PLIP) NA.17: 4 residues within 4Å: Chain B: S.126, I.129, D.130, S.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.126 NA.18: 3 residues within 4Å: Chain B: A.60 Ligands: FAD.12, FLC.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.60

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.8: 4 residues within 4Å: Chain A: G.273, H.294 Chain B: N.182, D.184 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.182, B:D.184 IPA.9: 4 residues within 4Å: Chain A: A.47, G.52, E.54, D.198 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.54 IPA.10: 2 residues within 4Å: Chain A: F.108, F.109 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.108 IPA.19: 4 residues within 4Å: Chain A: N.182, D.184 Chain B: G.273, H.294 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.182, A:D.184 IPA.20: 4 residues within 4Å: Chain B: A.47, G.52, E.54, D.198 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.54 IPA.21: 2 residues within 4Å: Chain B: F.108, F.109 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.108

2 x FLC: CITRATE ANION(Non-covalent)

FLC.11: 9 residues within 4Å: Chain A: A.60, L.62, Y.187, F.188, V.276, R.288, H.290 Ligands: FAD.1, NA.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.187 Water bridges: A:H.85, A:Y.187, A:R.288, A:R.288, A:R.288, A:R.288, A:R.288 Salt bridges: A:R.288, A:R.288, A:H.290 FLC.22: 9 residues within 4Å: Chain B: A.60, L.62, Y.187, F.188, V.276, R.288, H.290 Ligands: FAD.12, NA.18 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.187 Water bridges: B:H.85, B:Y.187, B:R.288, B:R.288, B:R.288, B:R.288, B:R.288, B:Y.326 Salt bridges: B:R.288, B:R.288, B:H.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wangkanont, K. et al., Conformational Control of UDP-Galactopyranose Mutase Inhibition. Biochemistry (2017)

Release Date

2016-06-01

Peptides

UDP-galactopyranose mutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-galactopyranose mutase

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