SMTL ID : 6c4j.2 (1 other biounit)

Ligand bound full length hUGDH with A104L substitution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-hexamer

Ligands

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, E.161, L.163, E.165, S.275, C.276, K.279, R.346 Ligands: UPG.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:V.15, A:E.161 Hydrogen bonds: A:Y.14, A:V.15, A:V.37, A:R.41, A:R.41, A:V.89, A:N.90, A:T.91, A:T.131, A:E.165, A:S.275, A:K.279, A:K.279, A:R.346 Water bridges: A:G.13, A:G.16, A:R.41, A:R.41, A:A.111, A:R.115, A:T.131, A:R.346, A:R.346 Salt bridges: A:R.41, A:R.346, A:R.346 NAD.6: 20 residues within 4Å: Chain B: 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, S.130, T.131, E.161, L.163, K.220, K.279 Ligands: UPG.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.15, B:E.161 Hydrogen bonds: B:Y.14, B:V.15, B:V.37, B:R.41, B:R.41, B:V.89, B:N.90, B:T.91, B:T.131, B:K.279, B:K.279 Salt bridges: B:R.41 NAD.9: 23 residues within 4Å: Chain C: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, E.161, L.163, E.165, K.220, S.275 Ligands: UPG.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.14, C:V.15, C:V.37, C:R.41, C:R.41, C:V.89, C:T.91, C:Y.108, C:T.131, C:E.165, C:E.165, C:S.275 Water bridges: C:G.13 Salt bridges: C:R.41 NAD.13: 25 residues within 4Å: Chain D: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, A.111, S.130, T.131, E.161, L.163, E.165, S.275, C.276, K.279, R.346 Ligands: UPG.14 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:V.15, D:E.161 Hydrogen bonds: D:Y.14, D:V.15, D:V.37, D:R.41, D:R.41, D:V.89, D:N.90, D:T.91, D:Y.108, D:T.131, D:E.165, D:S.275, D:K.279, D:K.279, D:R.346 Water bridges: D:R.41, D:R.41, D:R.115, D:R.346, D:R.346 Salt bridges: D:R.41, D:R.346, D:R.346 NAD.16: 22 residues within 4Å: Chain E: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, E.161, L.163, K.220, C.276, K.279 Ligands: UPG.17 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:V.15, E:E.161 Hydrogen bonds: E:Y.14, E:V.15, E:V.37, E:R.41, E:R.41, E:V.89, E:T.91, E:T.131, E:K.279, E:K.279 Water bridges: E:G.13, E:G.16 Salt bridges: E:R.41 NAD.22: 21 residues within 4Å: Chain F: 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, E.161, L.163, C.276, K.279 Ligands: UPG.23 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.15, F:E.161 Hydrogen bonds: F:Y.14, F:V.15, F:V.37, F:R.41, F:N.90, F:T.91, F:T.131, F:K.279 Salt bridges: F:R.41

6 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.2: 22 residues within 4Å: Chain A: 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 Chain B: R.260 Ligands: NAD.1 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.231, A:F.265 Hydrogen bonds: A:F.162, A:E.165, A:K.220, A:N.224, A:K.267, A:K.267, A:S.269, A:G.273, A:F.338, A:E.416, A:R.442, A:R.442, B:R.260, B:R.260 Water bridges: A:K.220, A:C.276, A:D.280 Salt bridges: A:K.339, A:K.339 UPG.7: 20 residues within 4Å: Chain A: R.260 Chain B: 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 Ligands: NAD.6 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.231, B:F.265 Hydrogen bonds: B:F.162, B:E.165, B:K.220, B:N.224, B:K.267, B:K.267, B:S.269, B:G.273, B:F.338, B:R.442, B:R.442, A:R.260, A:R.260 Water bridges: B:F.265 Salt bridges: B:K.339, B:K.339 UPG.10: 21 residues within 4Å: Chain C: 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 Chain D: R.260 Ligands: NAD.9 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:F.162, C:E.165, C:K.220, C:N.224, C:K.267, C:K.267, C:S.269, 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 UPG.14: 22 residues within 4Å: Chain C: R.260 Chain D: 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 Ligands: NAD.13 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.231, D:F.265 Hydrogen bonds: D:F.162, D:E.165, D:K.220, D:N.224, D:K.267, D:K.267, D:S.269, D:G.273, D:D.280, D:D.280, D:F.338, D:E.416, D:R.442, D:R.442, C:R.260, C:R.260 Water bridges: D:C.276 Salt bridges: D:K.339, D:K.339 UPG.17: 22 residues within 4Å: Chain E: 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 Chain F: R.260 Ligands: NAD.16 21 PLIP interactions: 19 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.231, E:F.265 Hydrogen bonds: E:F.162, E:E.165, E:K.220, E:N.224, E:K.267, E:K.267, E:K.267, E:S.269, E:G.273, E:F.338, E:E.416, E:R.442, E:R.442, F:R.260, F:R.260 Water bridges: E:R.177, E:C.276 Salt bridges: E:K.339, E:K.339 UPG.23: 21 residues within 4Å: Chain E: R.260 Chain F: 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 Ligands: NAD.22 19 PLIP interactions: 17 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.231, F:F.265 Hydrogen bonds: F:F.162, F:E.165, F:K.220, F:N.224, F:K.267, F:K.267, F:S.269, F:G.273, F:F.338, F:E.416, F:R.442, F:R.442, E:R.260, E:R.260 Water bridges: F:C.276 Salt bridges: F:K.339, F:K.339

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.135, W.214 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.135, W.214 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: G.99, R.102 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: R.135 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain D: R.135, W.214 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain E: G.56 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain E: G.99, R.102 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain F: R.135, W.214 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: R.312 Chain F: G.99, R.102 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: N.263, K.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.263 Salt bridges: A:K.264 SO4.20: 4 residues within 4Å: Chain E: R.135, W.214 Chain F: G.245, K.465 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Salt bridges: F:K.465, E:R.135

3 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.5: 6 residues within 4Å: Chain A: F.162, D.171, D.176, R.177 Chain B: D.258, R.260 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.258, B:R.260 Water bridges: A:D.176 PGO.21: 6 residues within 4Å: Chain E: F.162, D.171, D.176, R.177 Chain F: D.258, R.260 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.176 Water bridges: E:D.171 PGO.26: 5 residues within 4Å: Chain E: D.258, R.260 Chain F: F.162, D.171, D.176 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:D.176 Hydrogen bonds: F:F.162, E:D.258, E:R.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beattie, N.R. et al., Hysteresis and Allostery in Human UDP-Glucose Dehydrogenase Require a Flexible Protein Core. Biochemistry (2018)

Release Date

2018-05-16

Peptides

UDP-glucose 6-dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

UDP-glucose 6-dehydrogenase

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