SMTL ID : 3prj.1

Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

6 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 21 residues within 4Å: Chain A: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:K.279 Hydrogen bonds: A:Y.14, A:V.15, A:V.37, A:R.41, A:R.41, A:N.90, A:T.91, A:Y.108, A:S.130, A:T.131, A:V.132, A:S.275, A:K.279, A:R.346 Water bridges: A:G.13, A:G.13, A:R.41, A:R.41 Salt bridges: A:R.41, A:R.346, A:R.346 NAI.3: 22 residues within 4Å: Chain B: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.279 Hydrogen bonds: B:Y.14, B:V.15, B:V.37, B:R.41, B:R.41, B:N.90, B:T.91, B:Y.108, B:S.130, B:T.131, B:V.132, B:S.275, B:K.279 Salt bridges: B:R.41, B:R.346, B:R.346 NAI.5: 23 residues within 4Å: Chain C: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, S.88, V.89, N.90, T.91, P.92, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:N.90 Hydrogen bonds: C:Y.14, C:V.15, C:V.37, C:R.41, C:R.41, C:N.90, C:T.91, C:T.131, C:V.132, C:S.275, C:K.279, C:R.346 Water bridges: C:N.38 Salt bridges: C:R.41, C:R.346, C:R.346 NAI.7: 20 residues within 4Å: Chain D: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.14, D:V.15, D:G.16, D:V.37, D:R.41, D:R.41, D:N.90, D:T.91, D:T.131, D:V.132, D:S.275, D:K.279, D:R.346 Salt bridges: D:R.41, D:R.346, D:R.346 NAI.9: 22 residues within 4Å: Chain E: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, P.92, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:K.279 Hydrogen bonds: E:Y.14, E:V.15, E:V.37, E:R.41, E:R.41, E:N.90, E:Y.108, E:S.130, E:T.131, E:V.132, E:K.279 Water bridges: E:R.41 Salt bridges: E:R.41, E:R.346, E:R.346 NAI.11: 21 residues within 4Å: Chain F: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:K.279 Hydrogen bonds: F:Y.14, F:V.15, F:V.37, F:R.41, F:R.41, F:N.90, F:Y.108, F:T.131, F:S.275, F:K.279 Water bridges: F:G.13, F:G.13 Salt bridges: F:R.41, F:R.346, F:R.346

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

UDX.2: 21 residues within 4Å: Chain A: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 Chain B: R.260 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.231 Hydrogen bonds: A:E.165, A:K.220, A:K.220, A:K.267, A:K.267, A:S.269, A:G.273, A:F.338, A:R.442, A:R.442, B:R.260, B:R.260 Salt bridges: A:K.339, A:K.339 pi-Stacking: A:F.265 UDX.4: 22 residues within 4Å: Chain A: R.260 Chain B: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, L.227, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.265 Hydrogen bonds: B:E.165, B:K.220, B:K.220, B:K.267, B:K.267, B:S.269, B:G.273, B:G.273, B:F.338, B:R.442, B:R.442, A:R.260, A:R.260 Salt bridges: B:K.339, B:K.339 UDX.6: 21 residues within 4Å: Chain C: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 Chain D: R.260 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.231 Hydrogen bonds: C:L.163, C:E.165, C:K.220, C:K.220, C:K.267, C:K.267, C:S.269, C:G.273, C:G.273, C:F.338, C:R.442, C:R.442, D:R.260, D:R.260 Salt bridges: C:K.339, C:K.339 pi-Stacking: C:F.265 UDX.8: 22 residues within 4Å: Chain C: R.260 Chain D: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, E.416, R.442 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.265 Hydrogen bonds: D:E.165, D:K.220, D:K.220, D:K.267, D:K.267, D:S.269, D:G.273, D:E.416, D:R.442, D:R.442, C:R.260, C:R.260 Water bridges: D:F.272, D:F.338 Salt bridges: D:K.339, D:K.339 UDX.10: 23 residues within 4Å: Chain E: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, L.227, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, E.416, R.442 Chain F: R.260 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.231, E:F.265 Hydrogen bonds: E:T.131, E:F.162, E:E.165, E:K.220, E:K.267, E:K.267, E:S.269, E:G.273, E:E.416, E:R.442, E:R.442, F:R.260, F:R.260 Water bridges: E:R.177 Salt bridges: E:K.339, E:K.339 UDX.12: 21 residues within 4Å: Chain E: R.260 Chain F: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 18 PLIP interactions: 16 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.231, F:F.265 Hydrogen bonds: F:T.131, F:F.162, F:E.165, F:K.220, F:K.267, F:K.267, F:S.269, F:G.273, F:G.273, F:F.338, F:R.442, F:R.442, E:R.260, E:R.260 Salt bridges: F:K.339, F:K.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase. Biochemistry (2011)

Release Date

2011-06-15

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

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