SMTL ID : 5lnt.1

Crystal structure of Arabidopsis thaliana Pdx1K166R-preI320 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-12-mer

Ligands

12 x KPR: [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate(Covalent)

KPR.1: 18 residues within 4Å: Chain A: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.66, A:K.98, A:V.123 Hydrogen bonds: A:D.41, A:D.119, A:G.170, A:G.230, A:G.231, A:G.252, A:S.253 Water bridges: A:T.171, A:V.232, A:V.232, A:G.254, A:G.254 KPR.3: 18 residues within 4Å: Chain B: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.66, B:K.98, B:V.123 Hydrogen bonds: B:D.41, B:D.119, B:G.170, B:G.230, B:G.231, B:G.252, B:S.253 Water bridges: B:T.171, B:T.171, B:V.232, B:V.232, B:G.254 KPR.5: 18 residues within 4Å: Chain C: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:P.66, C:K.98, C:V.123 Hydrogen bonds: C:D.41, C:G.170, C:G.231, C:G.252, C:S.253 Water bridges: C:T.171, C:T.171, C:V.232, C:V.232, C:G.254 KPR.7: 18 residues within 4Å: Chain D: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:P.66, D:K.98, D:V.123 Hydrogen bonds: D:D.41, D:G.170, D:G.230, D:G.231, D:G.252, D:S.253, D:S.253 Water bridges: D:T.171, D:T.171, D:V.232, D:V.232, D:G.254 KPR.9: 18 residues within 4Å: Chain E: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:P.66, E:K.98, E:V.123 Hydrogen bonds: E:D.41, E:D.119, E:G.170, E:G.230, E:G.231, E:G.252, E:S.253 Water bridges: E:T.171, E:V.232, E:V.232, E:G.254, E:G.254 KPR.11: 18 residues within 4Å: Chain F: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:P.66, F:K.98, F:V.123 Hydrogen bonds: F:D.41, F:D.119, F:G.170, F:G.230, F:G.231, F:G.252, F:S.253 Water bridges: F:T.171, F:T.171, F:V.232, F:V.232, F:G.254 KPR.13: 18 residues within 4Å: Chain G: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:P.66, G:K.98, G:V.123 Hydrogen bonds: G:D.41, G:G.170, G:G.231, G:G.252, G:S.253 Water bridges: G:T.171, G:T.171, G:V.232, G:V.232, G:G.254 KPR.15: 18 residues within 4Å: Chain H: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:P.66, H:K.98, H:V.123 Hydrogen bonds: H:D.41, H:G.170, H:G.230, H:G.231, H:G.252, H:S.253, H:S.253 Water bridges: H:T.171, H:T.171, H:V.232, H:V.232, H:G.254 KPR.17: 18 residues within 4Å: Chain I: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain I Hydrophobic interactions: I:P.66, I:K.98, I:V.123 Hydrogen bonds: I:D.41, I:D.119, I:G.170, I:G.230, I:G.231, I:G.252, I:S.253 Water bridges: I:T.171, I:V.232, I:V.232, I:G.254, I:G.254 KPR.19: 18 residues within 4Å: Chain J: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:P.66, J:K.98, J:V.123 Hydrogen bonds: J:D.41, J:D.119, J:G.170, J:G.230, J:G.231, J:G.252, J:S.253 Water bridges: J:T.171, J:T.171, J:V.232, J:V.232, J:G.254 KPR.21: 18 residues within 4Å: Chain K: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:P.66, K:K.98, K:V.123 Hydrogen bonds: K:D.41, K:G.170, K:G.231, K:G.252, K:S.253 Water bridges: K:T.171, K:T.171, K:V.232, K:V.232, K:G.254 KPR.23: 18 residues within 4Å: Chain L: D.41, M.60, P.66, K.98, D.119, S.121, V.123, R.164, E.168, A.169, G.170, A.229, G.230, G.231, F.250, V.251, G.252, S.253 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:P.66, L:K.98, L:V.123 Hydrogen bonds: L:D.41, L:G.170, L:G.230, L:G.231, L:G.252, L:S.253, L:S.253 Water bridges: L:T.171, L:T.171, L:V.232, L:V.232, L:G.254

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

PO4.2: 5 residues within 4Å: Chain A: H.132, E.151, R.154, R.155 Chain D: K.204 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Salt bridges: A:H.132, A:R.154, A:R.155, D:K.204 Water bridges: D:K.204 PO4.4: 5 residues within 4Å: Chain B: H.132, E.151, R.154, R.155 Chain C: K.204 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Water bridges: B:H.132, C:T.201, C:K.204, C:K.204, C:K.204, C:K.204 Salt bridges: B:H.132, B:R.154, B:R.155, C:K.204 PO4.6: 5 residues within 4Å: Chain B: K.204 Chain C: H.132, E.151, R.154, R.155 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Water bridges: B:K.204, C:H.132, C:H.132, C:R.154, C:R.154 Salt bridges: B:K.204, C:H.132, C:R.154, C:R.155 Hydrogen bonds: C:E.151, C:E.151 PO4.8: 5 residues within 4Å: Chain A: K.204 Chain D: H.132, E.151, R.154, R.155 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Water bridges: D:H.132, D:H.132, A:K.204, A:K.204 Salt bridges: D:H.132, D:R.154, D:R.155, A:K.204 PO4.10: 5 residues within 4Å: Chain E: H.132, E.151, R.154, R.155 Chain H: K.204 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain H Salt bridges: E:H.132, E:R.154, E:R.155, H:K.204 Water bridges: H:K.204 PO4.12: 5 residues within 4Å: Chain F: H.132, E.151, R.154, R.155 Chain G: K.204 10 PLIP interactions: 4 interactions with chain F, 6 interactions with chain G Water bridges: F:H.132, G:T.201, G:K.204, G:K.204, G:K.204, G:K.204 Salt bridges: F:H.132, F:R.154, F:R.155, G:K.204 PO4.14: 5 residues within 4Å: Chain F: K.204 Chain G: H.132, E.151, R.154, R.155 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:E.151, G:E.151 Water bridges: G:H.132, G:H.132, G:R.154, G:R.154, F:K.204 Salt bridges: G:H.132, G:R.154, G:R.155, F:K.204 PO4.16: 5 residues within 4Å: Chain E: K.204 Chain H: H.132, E.151, R.154, R.155 8 PLIP interactions: 5 interactions with chain H, 3 interactions with chain E Water bridges: H:H.132, H:H.132, E:K.204, E:K.204 Salt bridges: H:H.132, H:R.154, H:R.155, E:K.204 PO4.18: 5 residues within 4Å: Chain I: H.132, E.151, R.154, R.155 Chain L: K.204 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain L Salt bridges: I:H.132, I:R.154, I:R.155, L:K.204 Water bridges: L:K.204 PO4.20: 5 residues within 4Å: Chain J: H.132, E.151, R.154, R.155 Chain K: K.204 10 PLIP interactions: 4 interactions with chain J, 6 interactions with chain K Water bridges: J:H.132, K:T.201, K:K.204, K:K.204, K:K.204, K:K.204 Salt bridges: J:H.132, J:R.154, J:R.155, K:K.204 PO4.22: 5 residues within 4Å: Chain J: K.204 Chain K: H.132, E.151, R.154, R.155 11 PLIP interactions: 9 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:E.151, K:E.151 Water bridges: K:H.132, K:H.132, K:R.154, K:R.154, J:K.204 Salt bridges: K:H.132, K:R.154, K:R.155, J:K.204 PO4.24: 5 residues within 4Å: Chain I: K.204 Chain L: H.132, E.151, R.154, R.155 8 PLIP interactions: 3 interactions with chain I, 5 interactions with chain L Water bridges: I:K.204, I:K.204, L:H.132, L:H.132 Salt bridges: I:K.204, L:H.132, L:R.154, L:R.155

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 PDX1.1: 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 PDX1.1