SMTL ID : 5vr8.1

Human UDP-Glucose Dehydrogenase with UDP-Xylose Bound to the Co-enzyme Site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

10 x UDX: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE(Non-covalent)

UDX.1: 20 residues within 4Å: Chain A: G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, S.89, V.90, N.91, T.92, Y.109, C.113, S.131, T.132, V.133, S.276, K.280, R.347 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.90, A:Y.109 Hydrogen bonds: A:Y.15, A:V.16, A:V.38, A:R.42, A:R.42, A:T.92, A:T.92, A:S.131, A:T.132, A:V.133, A:S.276, A:K.280 Water bridges: A:G.14, A:G.17, A:R.42, A:R.42, A:E.166, A:E.166, A:R.347, A:R.347 Salt bridges: A:R.42, A:R.347, A:R.347, A:R.347 UDX.2: 21 residues within 4Å: Chain A: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Chain B: R.261 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.232, A:F.266 Hydrogen bonds: A:F.163, A:E.166, A:K.221, A:K.268, A:K.268, A:S.270, A:G.274, A:G.274, A:F.339, A:R.443, A:R.443, B:R.261, B:R.261 Water bridges: A:F.266, A:C.277, A:C.277, A:K.340, A:K.340 Salt bridges: A:K.340, A:K.340 UDX.3: 20 residues within 4Å: Chain B: G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, S.89, V.90, N.91, T.92, Y.109, C.113, S.131, T.132, V.133, S.276, K.280, R.347 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.90, B:Y.109 Hydrogen bonds: B:Y.15, B:V.16, B:V.38, B:R.42, B:R.42, B:T.92, B:T.92, B:T.132, B:T.132, B:V.133, B:S.276 Water bridges: B:G.14, B:G.17, B:N.39, B:R.42, B:N.91, B:S.131, B:E.166, B:S.276, B:R.347 Salt bridges: B:R.42, B:R.347, B:R.347, B:R.347 UDX.4: 21 residues within 4Å: Chain A: R.261 Chain B: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.232, B:F.266 Hydrogen bonds: B:F.163, B:E.166, B:K.221, B:K.268, B:K.268, B:S.270, B:G.274, B:G.274, B:F.339, B:R.443, B:R.443, A:R.261, A:R.261 Water bridges: B:F.266, B:C.277, B:C.277, B:C.277, B:K.340, B:K.340 Salt bridges: B:K.340, B:K.340 UDX.6: 21 residues within 4Å: Chain C: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Chain E: R.261 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:I.232, C:F.266 Hydrogen bonds: C:F.163, C:E.166, C:K.221, C:K.268, C:K.268, C:S.270, C:G.274, C:G.274, C:F.339, C:R.443, C:R.443, E:R.261, E:R.261 Water bridges: C:F.266, C:C.277, C:C.277, C:K.340, C:K.340 Salt bridges: C:K.340, C:K.340 UDX.7: 20 residues within 4Å: Chain D: G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, S.89, V.90, N.91, T.92, Y.109, C.113, S.131, T.132, V.133, S.276, K.280, R.347 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:V.90, D:Y.109 Hydrogen bonds: D:Y.15, D:V.16, D:V.38, D:R.42, D:R.42, D:T.92, D:T.92, D:S.131, D:T.132, D:T.132, D:V.133, D:S.276 Water bridges: D:G.14, D:G.17, D:R.42, D:R.42, D:E.166, D:E.166, D:R.347, D:R.347 Salt bridges: D:R.42, D:R.347, D:R.347, D:R.347 UDX.8: 22 residues within 4Å: Chain D: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, L.228, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Chain F: R.261 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:I.232, D:F.266 Hydrogen bonds: D:F.163, D:E.166, D:K.221, D:K.268, D:K.268, D:S.270, D:G.274, D:G.274, D:F.339, D:R.443, D:R.443, F:R.261, F:R.261 Water bridges: D:F.266, D:C.277, D:C.277, D:K.340, D:K.340 Salt bridges: D:K.340, D:K.340 UDX.9: 19 residues within 4Å: Chain E: G.12, G.14, Y.15, V.16, D.37, V.38, R.42, S.89, V.90, N.91, T.92, Y.109, C.113, S.131, T.132, V.133, S.276, K.280, R.347 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:V.90, E:Y.109 Hydrogen bonds: E:Y.15, E:V.16, E:V.38, E:R.42, E:R.42, E:T.92, E:T.92, E:S.131, E:T.132, E:V.133, E:S.276 Water bridges: E:G.14, E:G.17, E:R.42, E:E.166, E:E.166 Salt bridges: E:R.42, E:R.347, E:R.347, E:R.347 UDX.10: 21 residues within 4Å: Chain C: R.261 Chain E: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 22 PLIP interactions: 20 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:I.232, E:F.266 Hydrogen bonds: E:F.163, E:E.166, E:K.221, E:K.268, E:K.268, E:S.270, E:G.274, E:G.274, E:F.339, E:R.443, E:R.443, C:R.261, C:R.261 Water bridges: E:F.266, E:C.277, E:K.340, E:K.340, E:K.340 Salt bridges: E:K.340, E:K.340 UDX.12: 22 residues within 4Å: Chain D: R.261 Chain F: T.132, E.162, F.163, L.164, A.165, E.166, K.221, N.225, L.228, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 23 PLIP interactions: 21 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:I.232, F:F.266 Hydrogen bonds: F:F.163, F:E.166, F:K.221, F:K.268, F:K.268, F:S.270, F:G.274, F:G.274, F:F.339, F:R.443, F:R.443, D:R.261, D:R.261 Water bridges: F:F.163, F:A.165, F:C.277, F:C.277, F:K.340, F:K.340 Salt bridges: F:K.340, F:K.340

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 14 residues within 4Å: Chain C: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, I.76, V.90, N.91, C.113, R.347 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.15, C:V.16, C:V.38, C:R.42, C:R.42 Water bridges: C:G.14, C:G.17, C:N.39, C:R.42, C:R.42, C:E.166, C:E.166 Salt bridges: C:R.42, C:R.347, C:R.347 ADP.11: 14 residues within 4Å: Chain F: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, I.76, V.90, N.91, C.113, R.347 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.15, F:V.16, F:V.38, F:R.42 Water bridges: F:G.14, F:G.14, F:S.276, F:S.276, F:S.276, F:S.276 Salt bridges: F:R.42, F:R.347, F:R.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keul, N.D. et al., The entropic force generated by intrinsically disordered segments tunes protein function. Nature (2018)

Release Date

2017-07-19

Peptides

UDP-glucose 6-dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UDP-glucose 6-dehydrogenase