SMTL ID : 6d2e.1

Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-galactopyranose (open, oxidized)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 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, L.259, Y.325, Y.326, G.357, R.358, Y.364, L.365, D.366, M.367, A.370 Ligands: GDU.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:L.259, A:Y.325, A:Y.364 Hydrogen bonds: 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.9: 35 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, L.259, Y.325, Y.326, G.357, R.358, Y.364, L.365, D.366, M.367, A.370 Ligands: GDU.10 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:L.259, B:Y.325, B:Y.364 Hydrogen bonds: 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: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

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

GDU.2: 17 residues within 4Å: Chain A: A.60, H.64, F.98, F.153, I.154, Y.157, T.158, Q.161, W.162, Y.187, F.188, N.278, N.280, R.288, Y.326, D.366 Ligands: FAD.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.98 Hydrogen bonds: A:A.60, A:H.64, A:F.153, A:T.158, A:T.158, A:Q.161, A:Q.161, A:Y.187, A:N.278, A:N.280, A:R.288, A:R.288 Salt bridges: A:R.288 pi-Stacking: A:Y.157 GDU.10: 17 residues within 4Å: Chain B: A.60, H.64, F.98, F.153, I.154, Y.157, T.158, Q.161, W.162, Y.187, F.188, N.278, N.280, R.288, Y.326, D.366 Ligands: FAD.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.98 Hydrogen bonds: B:A.60, B:H.64, B:F.153, B:Y.157, B:T.158, B:Q.161, B:Q.161, B:N.278, B:N.280, B:R.288, B:R.288, B:Y.326 Water bridges: B:Y.187, B:Y.187 Salt bridges: B:R.288 pi-Stacking: B:Y.157

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

NA.3: 3 residues within 4Å: Chain A: S.126, I.129, S.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.143 NA.11: 3 residues within 4Å: Chain B: S.126, I.129, S.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.126

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

IPA.4: 2 residues within 4Å: Chain A: F.108, F.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.108 IPA.5: 4 residues within 4Å: Chain A: N.75, Q.76, F.77, A.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.76 IPA.6: 2 residues within 4Å: Chain A: F.271, K.312 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.271, A:F.271 Hydrogen bonds: A:E.264, A:K.312 IPA.7: 3 residues within 4Å: Chain A: D.260, E.262, Y.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.260, A:D.260 IPA.8: 6 residues within 4Å: Chain A: E.54, H.56, H.61, Y.200, F.292, F.295 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.292, A:F.295, A:F.295 Hydrogen bonds: A:E.54 IPA.12: 2 residues within 4Å: Chain B: F.108, F.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.108 IPA.13: 4 residues within 4Å: Chain B: N.75, Q.76, F.77, A.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.76 IPA.14: 2 residues within 4Å: Chain B: F.271, K.312 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.271, B:F.271 Hydrogen bonds: B:E.264, B:K.312 IPA.15: 3 residues within 4Å: Chain B: D.260, E.262, Y.314 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.260 IPA.16: 6 residues within 4Å: Chain B: E.54, H.56, H.61, Y.200, F.292, F.295 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.292, B:F.295, B:F.295 Hydrogen bonds: B:E.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wangkanont, K. et al., Substrate recognition by FAD in UDP-galactopyranose mutase. To be published

Release Date

2019-04-17

Peptides

UDP-galactopyranose mutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-galactopyranose mutase

Related Entries With Identical Sequence