SMTL ID : 4adu.1

Crystal structure of plasmodial PLP synthase with bound R5P intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-12-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain G: Y.116 Ligands: EDO.2, EDO.4 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: Y.176, F.188 Ligands: EDO.1, EDO.4 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain B: Y.176 Ligands: EDO.4, EDO.5 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Ligands: EDO.1, EDO.2, EDO.3, EDO.5 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain B: E.173, Y.176 Ligands: EDO.3, EDO.4 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain K: Y.116 Ligands: EDO.9, EDO.11 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain C: Y.176, F.188 Ligands: EDO.8, EDO.11 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain D: Y.176 Ligands: EDO.11, EDO.12 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Ligands: EDO.8, EDO.9, EDO.10, EDO.12 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain D: E.173, Y.176 Ligands: EDO.10, EDO.11 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain I: Y.116 Ligands: EDO.16, EDO.18 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain E: Y.176, F.188 Ligands: EDO.15, EDO.18 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain F: Y.176 Ligands: EDO.18, EDO.19 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Ligands: EDO.15, EDO.16, EDO.17, EDO.19 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain F: E.173, Y.176 Ligands: EDO.17, EDO.18 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: Y.116 Ligands: EDO.23, EDO.25 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain G: Y.176, F.188 Ligands: EDO.22, EDO.25 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain H: Y.176 Ligands: EDO.25, EDO.26 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Ligands: EDO.22, EDO.23, EDO.24, EDO.26 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain H: E.173, Y.176 Ligands: EDO.24, EDO.25 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain E: Y.116 Ligands: EDO.30, EDO.32 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain I: Y.176, F.188 Ligands: EDO.29, EDO.32 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain J: Y.176 Ligands: EDO.32, EDO.33 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Ligands: EDO.29, EDO.30, EDO.31, EDO.33 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain J: E.173, Y.176 Ligands: EDO.31, EDO.32 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: Y.116 Ligands: EDO.37, EDO.39 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain K: Y.176, F.188 Ligands: EDO.36, EDO.39 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain L: Y.176 Ligands: EDO.39, EDO.40 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Ligands: EDO.36, EDO.37, EDO.38, EDO.40 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain L: E.173, Y.176 Ligands: EDO.38, EDO.39 Ligand excluded by PLIP

12 x R5P: RIBOSE-5-PHOSPHATE(Post Translational Modification)

R5P.6: 15 residues within 4Å: Chain A: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.84 Hydrogen bonds: A:D.27, A:E.108, A:E.108, A:G.156, A:G.217, A:G.238, A:S.239 Water bridges: A:G.158, A:G.216, A:I.218 R5P.7: 16 residues within 4Å: Chain B: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.84, B:V.109 Hydrogen bonds: B:D.27, B:K.84, B:D.105, B:E.108, B:G.156, B:G.217, B:G.238, B:S.239 Water bridges: B:G.216, B:I.218, B:G.240, B:G.240 R5P.13: 15 residues within 4Å: Chain C: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:K.84 Hydrogen bonds: C:D.27, C:E.108, C:E.108, C:G.156, C:G.217, C:G.238, C:S.239 Water bridges: C:G.158, C:G.216, C:I.218 R5P.14: 16 residues within 4Å: Chain D: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:K.84, D:V.109 Hydrogen bonds: D:D.27, D:K.84, D:D.105, D:E.108, D:G.156, D:G.217, D:G.238, D:S.239 Water bridges: D:G.216, D:I.218, D:G.240, D:G.240 R5P.20: 15 residues within 4Å: Chain E: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:K.84 Hydrogen bonds: E:D.27, E:E.108, E:G.156, E:G.217, E:G.238, E:S.239 Water bridges: E:G.158, E:G.216, E:I.218 R5P.21: 16 residues within 4Å: Chain F: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:K.84, F:V.109 Hydrogen bonds: F:D.27, F:D.105, F:D.105, F:E.108, F:G.156, F:G.217, F:G.238, F:S.239 Water bridges: F:G.216, F:I.218, F:G.240, F:G.240 R5P.27: 15 residues within 4Å: Chain G: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:K.84 Hydrogen bonds: G:D.27, G:E.108, G:G.156, G:G.217, G:G.238, G:S.239 Water bridges: G:G.158, G:G.216, G:I.218 R5P.28: 16 residues within 4Å: Chain H: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:K.84, H:V.109 Hydrogen bonds: H:D.27, H:D.105, H:D.105, H:E.108, H:G.156, H:G.217, H:G.238, H:S.239 Water bridges: H:G.216, H:I.218, H:G.240, H:G.240 R5P.34: 15 residues within 4Å: Chain I: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:K.84 Hydrogen bonds: I:D.27, I:E.108, I:E.108, I:G.156, I:G.217, I:G.238, I:S.239 Water bridges: I:G.158, I:G.216, I:I.218 R5P.35: 16 residues within 4Å: Chain J: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:K.84, J:V.109 Hydrogen bonds: J:D.27, J:K.84, J:D.105, J:E.108, J:G.156, J:G.217, J:G.238, J:S.239 Water bridges: J:G.216, J:I.218, J:G.240, J:G.240 R5P.41: 15 residues within 4Å: Chain K: D.27, P.52, K.84, D.105, S.107, R.150, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:K.84 Hydrogen bonds: K:D.27, K:E.108, K:G.156, K:G.217, K:G.238, K:S.239 Water bridges: K:G.158, K:G.216, K:I.218 R5P.42: 16 residues within 4Å: Chain L: D.27, P.52, K.84, D.105, S.107, E.108, V.109, K.152, A.155, G.156, G.216, G.217, F.236, V.237, G.238, S.239 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:K.84, L:V.109 Hydrogen bonds: L:D.27, L:D.105, L:D.105, L:E.108, L:G.156, L:G.217, L:G.238, L:S.239 Water bridges: L:G.216, L:I.218, L:G.240, L:G.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guedez, G. et al., Assembly of the Eukaryotic Plp-Synthase Complex from Plasmodium and Activation of the Pdx1 Enzyme. Structure (2012)

Release Date

2012-01-25

Peptides

PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE

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