SMTL ID : 4h1t.1

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-hexamer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: E.48, I.68, S.72 Chain B: E.48, I.68, S.72 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:I.68, B:S.72, A:E.48, A:I.68, A:S.72 Water bridges: A:S.72 NA.65: 6 residues within 4Å: Chain E: E.48, I.68, S.72 Chain F: E.48, I.68, S.72 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:E.48, F:I.68, F:S.72, E:I.68, E:I.68, E:S.72 Water bridges: E:S.72

43 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: E.246, R.249 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: R.177 Chain C: R.177 Chain E: R.177 Ligands: SO4.67 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: N.39 Ligands: EDO.11 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.35, L.36, M.37 Ligands: EDO.11, PEG.20 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: R.174, V.175, V.176, Q.180 Chain C: M.189 Ligands: EDO.45 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.24, G.25, D.26, R.29 Chain B: R.47 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: G.25, R.90, G.92, T.93 Chain B: R.47 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: G.104, G.147, A.148, R.239 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: R.114, L.115, D.116, L.120, M.125, R.178 Chain B: L.120 Chain F: E.126 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: E.35, M.37, P.40 Ligands: EDO.4, EDO.5 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Ligands: SO4.78 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: G.147 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.184, E.185 Chain E: Q.180 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: P.40, V.41, F.42, Y.52 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: K.234, A.238 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: I.219, L.233, K.234, E.237 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: D.26, A.28 Chain B: S.45, H.46 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: G.95, F.161, Q.165, F.194, E.195, M.196 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: Q.144, A.148, T.149, V.150 Ligands: SO4.30 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: A.28, Q.31 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain B: E.55, G.58, S.60 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain C: M.183, K.184, Q.187 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain A: Q.180 Chain C: K.184, E.185, D.188 Ligands: EDO.6 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain C: T.93, F.161, Q.165, F.194, E.195, M.196 Ligands: CL.42 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: F.133, T.137 Chain C: F.133, T.137 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain B: D.134 Chain C: K.140, Q.144 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain C: D.169, I.227 Chain D: Q.82 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain D: K.140, Q.144 Chain E: D.134 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain D: V.154, M.189, G.190, V.191 Chain E: F.127, A.206 Ligand excluded by PLIP EDO.60: 6 residues within 4Å: Chain D: P.24, G.25, D.26, R.29, G.92 Ligands: EOH.62 Ligand excluded by PLIP EDO.61: 5 residues within 4Å: Chain D: F.161, Q.165, F.194, E.195, M.196 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain E: F.6, R.47 Chain F: L.233 Ligand excluded by PLIP EDO.69: 2 residues within 4Å: Chain E: T.137, A.141 Ligand excluded by PLIP EDO.70: 6 residues within 4Å: Chain E: T.94, G.95, F.161, Q.165, R.167, F.194 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain E: P.27, S.45, R.47, T.50 Ligand excluded by PLIP EDO.72: 3 residues within 4Å: Chain D: M.125 Chain E: M.125, E.126 Ligand excluded by PLIP EDO.79: 7 residues within 4Å: Chain F: G.95, F.161, Q.165, F.194, E.195, M.196 Ligands: CL.77 Ligand excluded by PLIP EDO.80: 2 residues within 4Å: Chain F: N.102, Q.224 Ligand excluded by PLIP EDO.81: 3 residues within 4Å: Chain F: G.209, L.210, K.211 Ligand excluded by PLIP EDO.82: 4 residues within 4Å: Chain E: F.6 Chain F: P.228, H.230, L.233 Ligand excluded by PLIP EDO.83: 4 residues within 4Å: Chain E: D.26, A.28 Chain F: H.46, R.47 Ligand excluded by PLIP EDO.84: 2 residues within 4Å: Chain F: A.13, N.16 Ligand excluded by PLIP EDO.85: 5 residues within 4Å: Chain B: R.177 Chain F: Q.180, G.181, S.182, E.185 Ligand excluded by PLIP

6 x EOH: ETHANOL(Non-functional Binders)

EOH.12: 4 residues within 4Å: Chain A: H.46, R.47 Chain B: D.26, A.28 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.47, B:D.26 Water bridges: A:H.46 Hydrophobic interactions: B:A.28 EOH.19: 3 residues within 4Å: Chain A: Q.98, H.100, G.190 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.187, A:G.190 EOH.34: 2 residues within 4Å: Chain B: A.206, G.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.206, B:G.209 EOH.50: 3 residues within 4Å: Chain C: V.103, D.229, T.232 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.232 Hydrogen bonds: C:D.229, C:D.229 Water bridges: C:D.229 EOH.62: 5 residues within 4Å: Chain C: R.47 Chain D: G.25, R.90, T.93 Ligands: EDO.60 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.90, C:R.47, C:R.47 Water bridges: D:G.25, D:E.197 EOH.86: 6 residues within 4Å: Chain F: T.4, G.9, V.10, T.11, D.14 Ligands: PEG.88 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.4 Hydrogen bonds: F:T.11, F:D.14

28 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 2 residues within 4Å: Chain A: D.38 Ligands: EDO.5 Ligand excluded by PLIP PEG.21: 3 residues within 4Å: Chain A: P.99, H.100, N.102 Ligand excluded by PLIP PEG.22: 6 residues within 4Å: Chain A: E.12, A.81, Q.82, L.83, G.84, R.86 Ligand excluded by PLIP PEG.23: 6 residues within 4Å: Chain A: T.4, V.5, F.6, H.7, G.9, H.46 Ligand excluded by PLIP PEG.24: 5 residues within 4Å: Chain A: E.166, R.167, Y.168, D.169, R.222 Ligand excluded by PLIP PEG.25: 1 residues within 4Å: Chain A: R.86 Ligand excluded by PLIP PEG.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.37: 4 residues within 4Å: Chain B: K.140, H.151, M.152 Chain C: D.134 Ligand excluded by PLIP PEG.38: 4 residues within 4Å: Chain B: Q.180, G.181, K.184 Ligands: PEG.63 Ligand excluded by PLIP PEG.39: 7 residues within 4Å: Chain B: L.115, R.178, F.179, S.182, E.185, W.186 Chain D: R.177 Ligand excluded by PLIP PEG.51: 5 residues within 4Å: Chain C: Q.98, V.101, V.150, H.151, L.192 Ligand excluded by PLIP PEG.52: 3 residues within 4Å: Chain C: D.38, N.39, P.40 Ligand excluded by PLIP PEG.53: 2 residues within 4Å: Chain C: Y.168, G.173 Ligand excluded by PLIP PEG.54: 1 residues within 4Å: Chain C: K.225 Ligand excluded by PLIP PEG.55: 2 residues within 4Å: Chain C: R.178 Chain D: L.120 Ligand excluded by PLIP PEG.56: 5 residues within 4Å: Chain C: L.36, M.37, D.38, L.56, R.249 Ligand excluded by PLIP PEG.63: 6 residues within 4Å: Chain B: Q.180 Chain D: R.177, Q.180 Chain F: R.177 Ligands: SO4.29, PEG.38 Ligand excluded by PLIP PEG.64: 3 residues within 4Å: Chain C: Q.82 Chain D: D.169, T.170 Ligand excluded by PLIP PEG.73: 6 residues within 4Å: Chain E: E.166, R.167, Y.168, D.169, M.183, R.222 Ligand excluded by PLIP PEG.74: 3 residues within 4Å: Chain E: H.46, R.47 Chain F: D.26 Ligand excluded by PLIP PEG.75: 2 residues within 4Å: Chain E: K.184, Q.187 Ligand excluded by PLIP PEG.87: 2 residues within 4Å: Chain F: Y.168, G.173 Ligand excluded by PLIP PEG.88: 4 residues within 4Å: Chain F: G.9, A.44, H.46 Ligands: EOH.86 Ligand excluded by PLIP PEG.89: 8 residues within 4Å: Chain A: S.207, S.208, G.209 Chain B: R.174 Chain F: D.188, M.189, G.190 Ligands: PEG.93 Ligand excluded by PLIP PEG.90: 3 residues within 4Å: Chain F: F.42, S.45, T.50 Ligand excluded by PLIP PEG.91: 3 residues within 4Å: Chain F: E.35, L.36, M.37 Ligand excluded by PLIP PEG.92: 2 residues within 4Å: Chain F: Q.144, E.145 Ligand excluded by PLIP PEG.93: 5 residues within 4Å: Chain F: Q.98, Q.187, D.188, G.190 Ligands: PEG.89 Ligand excluded by PLIP

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.27: 7 residues within 4Å: Chain A: R.47 Chain B: G.25, R.29, R.90, V.91, G.92, T.93 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.25, B:D.26, B:V.91, B:T.93 Water bridges: B:R.90, B:T.93, B:T.93 Salt bridges: B:R.29, B:R.90, A:R.47 PO4.28: 1 residues within 4Å: Chain B: R.86 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.86, B:R.86 Salt bridges: B:R.86 PO4.40: 9 residues within 4Å: Chain C: P.24, G.25, D.26, R.29, R.90, V.91, G.92, T.93 Chain D: R.47 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Salt bridges: D:R.47, C:R.29, C:R.90 Hydrogen bonds: C:G.25, C:D.26, C:T.93, C:T.93 Water bridges: C:R.90 PO4.76: 8 residues within 4Å: Chain E: R.47 Chain F: G.25, D.26, R.29, R.90, V.91, G.92, T.93 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain F Salt bridges: E:R.47, F:R.29, F:R.90 Hydrogen bonds: F:G.25, F:D.26, F:T.93, F:T.93, F:T.93 Water bridges: F:R.90, F:R.90, F:R.90, F:R.90

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

SO4.29: 4 residues within 4Å: Chain B: R.177 Chain D: R.177 Chain F: R.177 Ligands: PEG.63 8 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F, 4 interactions with chain D Salt bridges: B:R.177, F:R.177, D:R.177 Water bridges: F:R.177, F:R.177, D:R.177, D:R.177, D:R.177 SO4.30: 3 residues within 4Å: Chain B: K.140, Q.144 Ligands: EDO.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.144 Salt bridges: B:K.140 SO4.43: 2 residues within 4Å: Chain C: R.239, K.242 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.239 Salt bridges: C:R.239, C:K.242 SO4.57: 2 residues within 4Å: Chain C: A.28 Chain D: H.46 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.47 Salt bridges: D:H.46 SO4.66: 4 residues within 4Å: Chain E: G.25, G.92, T.93 Chain F: R.47 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.93, E:T.93 Water bridges: E:G.25, E:D.26, E:R.90 Salt bridges: F:R.47 SO4.67: 4 residues within 4Å: Chain C: R.177 Chain E: R.177, Q.180 Ligands: EDO.3 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain E Salt bridges: C:R.177, E:R.177 Water bridges: E:R.177, E:R.177 SO4.78: 3 residues within 4Å: Chain F: K.140, Q.144 Ligands: EDO.13 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.144, F:Q.144 Water bridges: F:K.140, F:K.140, F:K.140 Salt bridges: F:K.140

1 x K: POTASSIUM ION(Non-covalent)

K.41: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:E.48, C:I.68, C:S.72, D:E.48, D:I.68

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

CL.42: 6 residues within 4Å: Chain C: G.95, F.161, Q.165, R.167, I.220 Ligands: EDO.46 Ligand excluded by PLIP CL.77: 6 residues within 4Å: Chain F: G.95, F.161, Q.165, R.167, I.220 Ligands: EDO.79 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution. TO BE PUBLISHED

Release Date

2013-09-11

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase

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