SMTL ID : 5lns.1

Crystal structure of Arabidopsis thaliana Pdx1-R5P complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-12-mer

Ligands

12 x 5RP: RIBULOSE-5-PHOSPHATE(Post Translational Modification)

5RP.1: 16 residues within 4Å: Chain A: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.97, A:V.122 Hydrogen bonds: A:D.40, A:D.118, A:G.169, A:G.230, A:G.251, A:S.252 Water bridges: A:G.229, A:V.231, A:G.253, A:G.253 5RP.3: 15 residues within 4Å: Chain B: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.97, B:V.122 Hydrogen bonds: B:D.40, B:D.118, B:G.169, B:G.230, B:G.251, B:S.252 Water bridges: B:G.229, B:V.231, B:G.253, B:G.253 5RP.5: 16 residues within 4Å: Chain C: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:K.97, C:V.122 Hydrogen bonds: C:D.40, C:G.169, C:G.230, C:G.251, C:S.252 Water bridges: C:G.229, C:V.231, C:G.253, C:G.253 5RP.7: 15 residues within 4Å: Chain D: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:P.65, D:K.97, D:V.122 Hydrogen bonds: D:D.40, D:K.97, D:G.169, D:G.230, D:G.251, D:S.252 Water bridges: D:G.229, D:V.231, D:G.253 5RP.9: 16 residues within 4Å: Chain E: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:K.97, E:V.122 Hydrogen bonds: E:D.40, E:D.118, E:G.169, E:G.230, E:G.251, E:S.252 Water bridges: E:G.229, E:V.231, E:G.253, E:G.253 5RP.11: 15 residues within 4Å: Chain F: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:K.97, F:V.122 Hydrogen bonds: F:D.40, F:D.118, F:G.169, F:G.230, F:G.251, F:S.252 Water bridges: F:G.229, F:V.231, F:G.253, F:G.253 5RP.13: 16 residues within 4Å: Chain G: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:K.97, G:V.122 Hydrogen bonds: G:D.40, G:G.169, G:G.230, G:G.251, G:S.252 Water bridges: G:G.229, G:V.231, G:G.253, G:G.253 5RP.15: 15 residues within 4Å: Chain H: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:P.65, H:K.97, H:V.122 Hydrogen bonds: H:D.40, H:K.97, H:G.169, H:G.230, H:G.251, H:S.252 Water bridges: H:G.229, H:V.231, H:G.253 5RP.17: 16 residues within 4Å: Chain I: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:K.97, I:V.122 Hydrogen bonds: I:D.40, I:D.118, I:G.169, I:G.230, I:G.251, I:S.252 Water bridges: I:G.229, I:V.231, I:G.253, I:G.253 5RP.19: 15 residues within 4Å: Chain J: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:K.97, J:V.122 Hydrogen bonds: J:D.40, J:D.118, J:G.169, J:G.230, J:G.251, J:S.252 Water bridges: J:G.229, J:V.231, J:G.253, J:G.253 5RP.21: 16 residues within 4Å: Chain K: D.40, M.59, P.65, K.97, D.118, S.120, V.122, R.163, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:K.97, K:V.122 Hydrogen bonds: K:D.40, K:G.169, K:G.230, K:G.251, K:S.252 Water bridges: K:G.229, K:V.231, K:G.253, K:G.253 5RP.23: 15 residues within 4Å: Chain L: D.40, M.59, P.65, K.97, D.118, S.120, V.122, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 12 PLIP interactions: 12 interactions with chain L Hydrophobic interactions: L:P.65, L:K.97, L:V.122 Hydrogen bonds: L:D.40, L:K.97, L:G.169, L:G.230, L:G.251, L:S.252 Water bridges: L:G.229, L:V.231, L:G.253

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

PO4.2: 5 residues within 4Å: Chain A: H.131, E.150, R.153, R.154 Chain D: K.203 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Water bridges: D:K.203, A:R.146, A:R.153, A:R.154 Salt bridges: D:K.203, A:H.131, A:R.153, A:R.154 Hydrogen bonds: A:E.150 PO4.4: 5 residues within 4Å: Chain B: H.131, E.150, R.153, R.154 Chain C: K.203 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:E.150, B:E.150 Water bridges: B:D.129, B:H.131, B:R.154, C:K.203, C:K.203 Salt bridges: B:H.131, B:R.153, B:R.154, C:K.203 PO4.6: 5 residues within 4Å: Chain B: K.203 Chain C: H.131, E.150, R.153, R.154 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Water bridges: C:D.129, C:H.131, C:H.131, C:E.157, B:K.203, B:K.203 Salt bridges: C:H.131, C:R.153, C:R.154, B:K.203 PO4.8: 5 residues within 4Å: Chain A: K.203 Chain D: H.131, E.150, R.153, R.154 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain D Water bridges: A:K.203, A:K.203, D:H.131, D:H.131, D:H.131, D:R.153, D:R.154 Salt bridges: A:K.203, D:H.131, D:R.153, D:R.154 Hydrogen bonds: D:E.150 PO4.10: 5 residues within 4Å: Chain E: H.131, E.150, R.153, R.154 Chain H: K.203 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:E.150 Water bridges: E:R.146, E:R.153, E:R.154, H:K.203 Salt bridges: E:H.131, E:R.153, E:R.154, H:K.203 PO4.12: 5 residues within 4Å: Chain F: H.131, E.150, R.153, R.154 Chain G: K.203 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:E.150, F:E.150 Water bridges: F:D.129, F:H.131, F:R.154, G:K.203, G:K.203 Salt bridges: F:H.131, F:R.153, F:R.154, G:K.203 PO4.14: 5 residues within 4Å: Chain F: K.203 Chain G: H.131, E.150, R.153, R.154 10 PLIP interactions: 7 interactions with chain G, 3 interactions with chain F Water bridges: G:D.129, G:H.131, G:H.131, G:E.157, F:K.203, F:K.203 Salt bridges: G:H.131, G:R.153, G:R.154, F:K.203 PO4.16: 5 residues within 4Å: Chain E: K.203 Chain H: H.131, E.150, R.153, R.154 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:E.150 Water bridges: H:H.131, H:H.131, H:H.131, H:R.153, H:R.154, E:K.203, E:K.203 Salt bridges: H:H.131, H:R.153, H:R.154, E:K.203 PO4.18: 5 residues within 4Å: Chain I: H.131, E.150, R.153, R.154 Chain L: K.203 9 PLIP interactions: 7 interactions with chain I, 2 interactions with chain L Hydrogen bonds: I:E.150 Water bridges: I:R.146, I:R.153, I:R.154, L:K.203 Salt bridges: I:H.131, I:R.153, I:R.154, L:K.203 PO4.20: 5 residues within 4Å: Chain J: H.131, E.150, R.153, R.154 Chain K: K.203 11 PLIP interactions: 8 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:E.150, J:E.150 Water bridges: J:D.129, J:H.131, J:R.154, K:K.203, K:K.203 Salt bridges: J:H.131, J:R.153, J:R.154, K:K.203 PO4.22: 5 residues within 4Å: Chain J: K.203 Chain K: H.131, E.150, R.153, R.154 10 PLIP interactions: 7 interactions with chain K, 3 interactions with chain J Water bridges: K:D.129, K:H.131, K:H.131, K:E.157, J:K.203, J:K.203 Salt bridges: K:H.131, K:R.153, K:R.154, J:K.203 PO4.24: 5 residues within 4Å: Chain I: K.203 Chain L: H.131, E.150, R.153, R.154 12 PLIP interactions: 3 interactions with chain I, 9 interactions with chain L Water bridges: I:K.203, I:K.203, L:H.131, L:H.131, L:H.131, L:R.153, L:R.154 Salt bridges: I:K.203, L:H.131, L:R.153, L:R.154 Hydrogen bonds: L:E.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, M.J. et al., Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat. Chem. Biol. (2017)

Release Date

2017-01-18

Peptides

Pyridoxal 5'-phosphate synthase subunit PDX1.3: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Pyridoxal 5'-phosphate synthase subunit PDX1.3

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