SMTL ID : 4lk3.1

Crystal structure of Human UDP-xylose synthase R236A substitution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 29 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, P.78, A.79, T.94, A.116, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.174, A:I.174 Hydrogen bonds: A:A.13, A:F.15, A:V.16, A:G.17, A:N.36, A:N.36, A:F.37, A:F.38, A:T.39, 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:A.79, A:K.151, A:T.177, A:R.188 Salt bridges: A:H.183 NAD.6: 31 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, K.90, T.94, A.116, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183, R.188 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.174, B:I.174 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:T.177, B:R.188 Water bridges: B:G.14, B:G.17 Salt bridges: B:H.183 NAD.11: 29 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, T.177, H.183, R.188 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:I.174 Hydrogen bonds: 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: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:R.188 Water bridges: C:G.14, C:G.17, C:T.177 Salt bridges: C:H.183 NAD.15: 31 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, 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 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.174 Hydrogen bonds: D:A.13, D:F.15, D:V.16, D:G.17, D:N.36, D:N.36, D:F.38, D:T.39, D:T.39, D:T.39, D:G.40, D:V.61, D:L.75, D:S.77, D:A.79, D:T.94, D:K.151, D:T.177, D:R.188 Salt bridges: D:H.183 NAD.20: 30 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, K.90, T.94, A.116, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183, R.188 25 PLIP interactions: 25 interactions with chain E Hydrophobic interactions: E:I.174, E:I.174 Hydrogen bonds: 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:D.60, E:V.61, E:L.75, E:S.77, E:K.90, E:K.151, E:T.177, E:T.177, E:R.188, E:R.188 Salt bridges: E:H.183 NAD.24: 29 residues within 4Å: Chain F: 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, S.117, T.118, K.151, I.174, F.175, N.176, T.177, H.183, R.188 25 PLIP interactions: 25 interactions with chain F Hydrophobic interactions: F:I.174 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:T.39, F:G.40, F:D.60, F:V.61, F:L.75, F:S.77, F:T.94, F:T.94, F:K.151, F:T.177, F:R.188, F:R.188 Salt bridges: F:H.183

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

UDP.2: 12 residues within 4Å: Chain A: N.176, G.187, R.188, V.189, N.192, F.193, T.204, V.205, Y.206, Q.211, R.213, I.247 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.176, A:G.187, A:V.189, A:N.192, A:T.204, A:T.204, A:Y.206, A:Q.211, A:R.213, A:R.213 Salt bridges: A:R.213, A:R.213 pi-Stacking: A:Y.206 UDP.7: 11 residues within 4Å: Chain B: G.187, R.188, V.189, N.192, F.193, T.204, V.205, Y.206, Q.211, R.213, I.247 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.189, B:N.192, B:T.204, B:Y.206, B:Q.211, B:R.213, B:R.213 Salt bridges: B:R.213 pi-Stacking: B:Y.206 UDP.16: 11 residues within 4Å: Chain D: N.176, R.188, V.189, N.192, F.193, T.204, V.205, Y.206, Q.211, R.213, I.247 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.176, D:V.189, D:N.192, D:T.204, D:Y.206, D:Q.211 Salt bridges: D:R.213, D:R.213 pi-Stacking: D:Y.206

6 x UGA: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID(Non-covalent)

UGA.3: 16 residues within 4Å: Chain A: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 Chain B: N.87, I.89, K.90, K.93 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.65, A:L.65, A:Y.66, A:R.108, A:Y.161, A:Y.161, A:Q.164, A:E.165, A:E.165, B:N.87 Salt bridges: A:K.107, A:K.107, A:K.107, B:K.90, B:K.93, B:K.93, B:K.93 UGA.8: 16 residues within 4Å: Chain A: N.87, I.89, K.90, K.93 Chain B: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.66 Hydrogen bonds: B:L.65, B:L.65, B:G.104, B:R.108, B:Q.164, B:E.165, A:N.87, A:N.87 Salt bridges: B:K.107, B:K.107, A:K.93, A:K.93, A:K.93 UGA.12: 16 residues within 4Å: Chain C: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 Chain D: N.87, I.89, K.90, K.93 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.66 Hydrogen bonds: C:L.65, C:L.65, C:R.108, C:Y.161, C:Y.161, C:Q.164, C:E.165, C:E.165, D:N.87 Salt bridges: C:K.107, C:K.107, C:K.107, D:K.90, D:K.93, D:K.93, D:K.93 UGA.17: 16 residues within 4Å: Chain C: N.87, I.89, K.90, K.93 Chain D: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.66 Hydrogen bonds: D:L.65, D:L.65, D:R.108, D:Y.161, D:Q.164, D:E.165, C:N.87 Salt bridges: D:K.107, D:K.107, D:K.107, C:K.93, C:K.93, C:K.93 UGA.22: 15 residues within 4Å: Chain E: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 Chain F: N.87, I.89, K.93 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:Y.66 Hydrogen bonds: E:L.65, E:L.65, E:G.104, E:R.108, E:Y.161, E:Q.164, E:E.165, E:E.165, F:N.87, F:N.87 Water bridges: E:K.107 Salt bridges: E:K.107, E:K.107, E:K.107, F:K.93, F:K.93, F:K.93 UGA.25: 15 residues within 4Å: Chain E: I.89, K.90, K.93 Chain F: P.64, L.65, Y.66, L.100, N.101, G.104, L.105, K.107, R.108, Y.161, Q.164, E.165 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:Y.66 Hydrogen bonds: F:L.65, F:L.65, F:R.108, F:Y.161, F:Q.164, F:E.165 Salt bridges: F:K.107, F:K.107, E:K.90, E:K.93, E:K.93, E:K.93

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

SO4.4: 4 residues within 4Å: Chain A: R.41, H.183, M.184, N.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.184, A:N.185, A:N.185 Salt bridges: A:R.41, A:H.183 SO4.5: 6 residues within 4Å: Chain A: R.41, K.42, R.43 Chain F: R.41, K.42, R.43 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:K.42, F:R.43, A:K.42, A:R.43 Salt bridges: F:R.43, A:R.43 SO4.9: 4 residues within 4Å: Chain B: R.41, H.183, M.184, N.185 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.184, B:N.185, B:N.185 Salt bridges: B:R.41, B:H.183 SO4.10: 6 residues within 4Å: Chain B: R.41, K.42, R.43 Chain C: R.41, K.42, R.43 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.42, C:R.43, B:K.42, B:R.43 Salt bridges: C:R.43, B:R.43 SO4.14: 4 residues within 4Å: Chain C: R.41, H.183, M.184, N.185 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:M.184, C:N.185, C:N.185 Water bridges: C:N.185 Salt bridges: C:R.41, C:H.183 SO4.18: 6 residues within 4Å: Chain D: R.41, K.42, R.43 Chain E: R.41, K.42, R.43 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:K.42, D:R.43, E:K.42, E:R.43 Salt bridges: D:R.43, E:R.43 SO4.19: 4 residues within 4Å: Chain D: R.41, H.183, M.184, N.185 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:M.184, D:N.185, D:N.185 Salt bridges: D:R.41, D:H.183 SO4.23: 5 residues within 4Å: Chain E: R.41, H.183, M.184, N.185, D.186 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.41, E:M.184, E:N.185, E:N.185 Salt bridges: E:H.183 SO4.27: 5 residues within 4Å: Chain F: R.41, H.183, M.184, N.185, D.186 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.41, F:M.184, F:N.185, F:N.185, F:N.185 Salt bridges: F:H.183

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

POP.13: 3 residues within 4Å: Chain C: R.188, V.189, R.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.189 Salt bridges: C:R.188, C:R.213 POP.21: 6 residues within 4Å: Chain E: E.120, N.176, G.187, R.188, V.189, R.213 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.176, E:V.189 Salt bridges: E:R.213 POP.26: 5 residues within 4Å: Chain F: N.176, R.188, V.189, R.213, F.215 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.176, F:G.187, F:V.189 Salt bridges: F:R.213, F:R.213

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

2013-08-07

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