SMTL ID : 4m55.1

Crystal structure of Human UDP-xylose synthase R236H substitution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.11, A.13, G.14, F.15, V.16, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, L.75, A.76, S.77, T.94, A.116, S.117, T.118, K.151, I.174, F.175, T.177, H.183, R.188 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.174 Hydrogen bonds: A:A.13, A:F.15, A:V.16, A:N.36, A:F.37, A:F.38, A:T.39, A:T.39, A:T.39, A:G.40, A:D.60, A:V.61, A:L.75, A:S.77, A:S.77, A:S.77, A:K.151, A:T.177, A:R.188 Salt bridges: A:H.183 NAD.4: 30 residues within 4Å: Chain B: G.11, A.13, G.14, F.15, V.16, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, L.75, A.76, S.77, P.78, A.79, T.94, A.116, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183, R.188 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:A.13, B:F.15, B:V.16, B:N.36, B:N.36, B:F.37, B:F.38, B:T.39, B:T.39, B:T.39, B:T.39, B:G.40, B:D.60, B:V.61, B:L.75, B:S.77, B:A.79, B:K.151, B:T.177, B:R.188, B:R.188 Salt bridges: B:H.183 NAD.7: 30 residues within 4Å: Chain C: G.11, A.13, G.14, F.15, V.16, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, L.75, A.76, S.77, P.78, A.79, T.94, A.116, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183, R.188 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.174, C:I.174 Hydrogen bonds: C:A.13, C:A.13, C:F.15, C:V.16, C:N.36, C:F.37, C:F.38, C:T.39, C:T.39, C:T.39, C:G.40, C:D.60, C:V.61, C:L.75, C:S.77, C:A.79, C:K.151, C:T.177, C:T.177, C:R.188, C:R.188 Salt bridges: C:H.183 NAD.10: 26 residues within 4Å: Chain D: G.11, A.13, G.14, F.15, V.16, G.17, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, L.75, A.76, S.77, T.94, A.116, T.118, K.151, I.174, F.175, T.177, H.183 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.174 Hydrogen bonds: D:A.13, D:A.13, D:F.15, D:V.16, D:G.17, D:N.36, D:F.37, D:F.38, D:T.39, D:T.39, D:G.40, D:D.60, D:D.60, D:V.61, D:L.75, D:S.77, D:K.151, D:T.177 Salt bridges: D:H.183 NAD.12: 25 residues within 4Å: Chain E: G.11, A.13, G.14, F.15, V.16, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, L.75, A.76, S.77, P.78, T.94, A.116, T.118, I.174, F.175, N.176, T.177 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:A.13, E:A.13, E:F.15, E:V.16, E:N.36, E:N.36, E:F.37, E:F.38, E:T.39, E:T.39, E:T.39, E:T.39, E:G.40, E:V.61, E:L.75, E:S.77, E:S.77, E:S.77, E:T.94, E:F.175, E:T.177 NAD.13: 20 residues within 4Å: Chain F: G.11, A.13, G.14, F.15, V.16, G.17, D.35, N.36, F.37, F.38, T.39, G.40, H.59, D.60, V.61, K.90, T.94, T.177, H.183, R.188 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:A.13, F:F.15, F:V.16, F:G.17, F:N.36, F:N.36, F:F.37, F:F.38, F:T.39, F:T.39, F:T.39, F:G.40, F:D.60, F:V.61, F:K.90, F:T.94, F:T.177, F:R.188 Salt bridges: F:H.183

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 4 residues within 4Å: Chain A: G.104, K.107, Y.161 Chain B: K.93 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.161 Salt bridges: A:K.107, B:K.93, B:K.93 POP.8: 4 residues within 4Å: Chain C: G.104, K.107, Y.161 Chain D: K.93 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.161, C:Y.161 Salt bridges: C:K.107, C:K.107, D:K.93, D:K.93

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

SO4.3: 3 residues within 4Å: Chain A: H.183, M.184, N.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.184, A:N.185, A:N.185 Salt bridges: A:H.183 SO4.6: 3 residues within 4Å: Chain B: H.183, M.184, N.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.184, B:N.185, B:N.185 Salt bridges: B:H.183 SO4.9: 3 residues within 4Å: Chain C: H.183, M.184, N.185 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:M.184, C:N.185, C:N.185 Salt bridges: C:H.183

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

UDP.5: 11 residues within 4Å: Chain A: K.93 Chain B: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.66, B:R.108 Hydrogen bonds: B:L.65, B:L.65, B:Y.66, B:R.108 Salt bridges: B:K.107, B:K.107, A:K.93, A:K.93 UDP.11: 7 residues within 4Å: Chain C: K.93 Chain D: P.64, L.100, N.101, G.104, K.107, Y.161 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.101, D:N.101, D:Y.161 Salt bridges: D:K.107, C:K.93, C:K.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walsh Jr., R.M. et al., Man o' war mutation in UDP-alpha-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation. Biochemistry (2015)

Release Date

2013-08-28

Peptides

UDP-glucuronic acid decarboxylase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UDP-glucuronic acid decarboxylase 1