SMTL ID : 3hdy.6 (5 other biounits)

Crystal Structure of UDP-galactopyranose mutase (reduced form) in complex with substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

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

GDU.1: 23 residues within 4Å: Chain A: I.86, H.88, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:F.175, A:T.180, A:T.180, A:T.180, A:R.198, A:Y.209, A:T.294, A:N.296, A:R.305, A:Y.370, A:Y.370 Water bridges: A:R.364 Salt bridges: A:R.198, A:R.198, A:R.305, A:R.305 pi-Stacking: A:Y.179 GDU.3: 20 residues within 4Å: Chain B: P.84, H.109, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, N.296, R.305, Y.335, Y.370, N.372 Ligands: FDA.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.175, B:T.180, B:T.180, B:R.198, B:Y.209, B:T.294, B:T.294, B:N.296, B:R.305, B:Y.370, B:Y.370 Water bridges: B:R.198 Salt bridges: B:R.198, B:R.198, B:R.305, B:R.305 pi-Stacking: B:Y.179 GDU.6: 20 residues within 4Å: Chain C: I.86, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, N.296, R.305, Y.335, Y.370 Ligands: FAD.5 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:F.175, C:T.180, C:T.180, C:T.180, C:W.184, C:R.198, C:Y.209, C:Y.209, C:T.294, C:N.296, C:Y.370, C:Y.370 Water bridges: C:R.305 Salt bridges: C:R.198, C:R.198, C:R.305, C:R.305 pi-Stacking: C:Y.179 GDU.7: 22 residues within 4Å: Chain D: P.84, H.109, I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FDA.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:F.175, D:T.180, D:T.180, D:R.198, D:T.294, D:N.296, D:Y.335, D:Y.370 Water bridges: D:R.305 Salt bridges: D:R.198, D:R.198, D:R.305, D:R.305 pi-Stacking: D:Y.179 GDU.10: 22 residues within 4Å: Chain E: P.84, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.9 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:F.175, E:T.180, E:T.180, E:R.198, E:Y.209, E:Y.209, E:T.294, E:T.294, E:N.296, E:R.305, E:Y.335, E:Y.370 Salt bridges: E:R.198, E:R.198, E:R.305, E:R.305 pi-Stacking: E:Y.179 GDU.12: 24 residues within 4Å: Chain F: P.84, H.88, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.11 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:F.175, F:T.180, F:T.180, F:R.198, F:Y.209, F:T.294, F:T.294, F:N.296, F:R.305, F:Y.335, F:Y.370 Salt bridges: F:R.198, F:R.198, F:R.305, F:R.305 pi-Stacking: F:Y.179 GDU.13: 21 residues within 4Å: Chain G: I.86, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, N.296, R.305, Y.335, Y.370, N.372 Ligands: FDA.14 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:H.109, G:F.175, G:T.180, G:T.180, G:R.198, G:Y.209, G:Y.209, G:N.296, G:R.305, G:Y.370, G:Y.370 Water bridges: G:R.198, G:R.198 Salt bridges: G:R.198, G:R.198, G:R.305, G:R.305 pi-Stacking: G:Y.179 GDU.16: 23 residues within 4Å: Chain H: P.84, I.86, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.15 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:F.175, H:T.180, H:T.180, H:W.184, H:R.198, H:Y.209, H:T.294, H:T.294, H:N.296, H:R.305, H:Y.335, H:Y.370 Water bridges: H:Y.179, H:Q.183, H:Y.370 Salt bridges: H:R.198, H:R.305, H:R.305 pi-Stacking: H:Y.179 GDU.18: 22 residues within 4Å: Chain I: H.88, H.109, V.111, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.17 19 PLIP interactions: 19 interactions with chain I Hydrogen bonds: I:F.175, I:T.180, I:T.180, I:Q.183, I:R.198, I:T.294, I:N.296, I:R.305, I:Y.335, I:Y.370, I:Y.370 Water bridges: I:R.198, I:R.198, I:R.364 Salt bridges: I:R.198, I:R.198, I:R.305, I:R.305 pi-Stacking: I:Y.179 GDU.20: 22 residues within 4Å: Chain J: P.84, I.86, H.109, I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, T.294, N.296, R.305, Y.335, Y.370, N.372 Ligands: FAD.19 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:F.175, J:T.180, J:T.180, J:T.180, J:R.198, J:T.294, J:N.296, J:R.305, J:Y.370, J:Y.370 Salt bridges: J:R.198, J:R.198, J:R.305, J:R.305 pi-Stacking: J:Y.179

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

FAD.2: 33 residues within 4Å: Chain A: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.277, A:Y.334 Hydrogen bonds: A:G.38, A:F.39, A:A.40, A:R.60, A:R.60, A:R.61, A:R.61, A:N.67, A:N.67, A:H.85, A:I.86, A:I.86, A:D.242, A:Y.243, A:T.258, A:R.364, A:Y.371, A:M.373 Water bridges: A:G.41, A:A.68, A:A.68, A:L.365, A:L.365 pi-Stacking: A:H.85, A:H.85 FAD.5: 33 residues within 4Å: Chain C: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.6 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.277, C:Y.334 Hydrogen bonds: C:G.38, C:F.39, C:A.40, C:R.60, C:R.61, C:R.61, C:N.67, C:N.67, C:H.85, C:I.86, C:I.86, C:D.242, C:Y.243, C:R.364, C:Y.371, C:M.373 pi-Stacking: C:H.85, C:H.85 FAD.9: 32 residues within 4Å: Chain E: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, T.258, G.259, P.260, L.277, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.10 26 PLIP interactions: 26 interactions with chain E Hydrophobic interactions: E:L.277, E:Y.334 Hydrogen bonds: E:G.38, E:F.39, E:A.40, E:R.60, E:R.61, E:R.61, E:N.67, E:N.67, E:H.85, E:I.86, E:I.86, E:D.242, E:Y.243, E:R.364, E:Y.371, E:M.373 Water bridges: E:A.37, E:G.41, E:G.66, E:A.68, E:T.258, E:D.374 pi-Stacking: E:H.85, E:H.85 FAD.11: 34 residues within 4Å: Chain F: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, E.325, Y.334, Y.335, G.363, R.364, L.365, Y.371, N.372, M.373, V.376 Ligands: GDU.12 25 PLIP interactions: 25 interactions with chain F Hydrophobic interactions: F:L.277, F:Y.334 Hydrogen bonds: F:G.38, F:F.39, F:A.40, F:R.60, F:R.60, F:R.61, F:R.61, F:N.67, F:H.85, F:I.86, F:I.86, F:D.242, F:Y.243, F:T.258, F:R.364, F:Y.371, F:M.373 Water bridges: F:G.66, F:A.68, F:A.68, F:D.374 pi-Stacking: F:H.85, F:H.85 FAD.15: 32 residues within 4Å: Chain H: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, T.258, G.259, P.260, L.277, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.16 27 PLIP interactions: 27 interactions with chain H Hydrophobic interactions: H:L.277, H:Y.334 Hydrogen bonds: H:G.38, H:F.39, H:A.40, H:R.60, H:R.61, H:R.61, H:N.67, H:N.67, H:H.85, H:I.86, H:I.86, H:D.242, H:Y.243, H:T.258, H:R.364, H:Y.371, H:M.373 Water bridges: H:G.41, H:A.68, H:A.68, H:L.365, H:L.365, H:D.374 pi-Stacking: H:H.85, H:H.85 FAD.17: 31 residues within 4Å: Chain I: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, T.258, G.259, P.260, L.277, E.325, Y.334, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.18 27 PLIP interactions: 27 interactions with chain I Hydrophobic interactions: I:L.277, I:Y.334 Hydrogen bonds: I:G.38, I:F.39, I:A.40, I:R.60, I:R.60, I:R.61, I:R.61, I:N.67, I:H.85, I:I.86, I:I.86, I:D.242, I:Y.243, I:R.364, I:Y.371, I:M.373 Water bridges: I:G.41, I:G.66, I:A.68, I:H.88, I:T.258, I:L.365, I:L.365 pi-Stacking: I:H.85, I:H.85 FAD.19: 33 residues within 4Å: Chain J: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, E.325, Y.335, G.363, R.364, L.365, Y.371, N.372, M.373, V.376 Ligands: GDU.20 23 PLIP interactions: 23 interactions with chain J Hydrophobic interactions: J:L.277 Hydrogen bonds: J:G.38, J:F.39, J:A.40, J:R.60, J:R.60, J:R.61, J:R.61, J:N.67, J:N.67, J:H.85, J:I.86, J:I.86, J:D.242, J:Y.243, J:R.244, J:R.364, J:Y.371, J:M.373 Water bridges: J:G.41, J:T.258 pi-Stacking: J:H.85, J:H.85

3 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.4: 32 residues within 4Å: Chain B: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, Y.334, Y.335, G.363, R.364, L.365, Y.371, N.372, M.373, V.376 Ligands: GDU.3 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.277, B:Y.334 Hydrogen bonds: B:G.38, B:F.39, B:A.40, B:R.60, B:R.60, B:R.61, B:R.61, B:N.67, B:N.67, B:N.67, B:P.84, B:H.85, B:I.86, B:I.86, B:D.242, B:Y.243, B:R.364, B:Y.371, B:M.373 Water bridges: B:L.365, B:L.365 pi-Stacking: B:H.85, B:H.85 FDA.8: 31 residues within 4Å: Chain D: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, T.241, D.242, Y.243, R.244, T.258, G.259, L.277, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.7 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:L.277, D:Y.334 Hydrogen bonds: D:G.38, D:F.39, D:A.40, D:R.60, D:R.61, D:N.67, D:N.67, D:N.67, D:P.84, D:H.85, D:I.86, D:I.86, D:D.242, D:Y.243, D:T.258, D:R.364, D:Y.371, D:M.373 Water bridges: D:G.41, D:R.60, D:A.68 pi-Stacking: D:H.85 FDA.14: 33 residues within 4Å: Chain G: V.35, G.36, G.38, F.39, A.40, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, L.277, R.305, E.325, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 Ligands: GDU.13 27 PLIP interactions: 27 interactions with chain G Hydrophobic interactions: G:L.277, G:Y.334 Hydrogen bonds: G:G.38, G:F.39, G:A.40, G:R.60, G:R.60, G:R.61, G:R.61, G:N.67, G:N.67, G:P.84, G:H.85, G:I.86, G:I.86, G:D.242, G:Y.243, G:T.258, G:R.364, G:Y.371, G:M.373 Water bridges: G:G.41, G:A.68, G:A.68, G:L.365, G:D.374 pi-Cation interactions: G:H.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Partha, S.K. et al., Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. J.Mol.Biol. (2009)

Release Date

2009-12-29

Peptides

UDP-galactopyranose mutase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

UDP-galactopyranose mutase

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