SMTL ID : 5lnw.1

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

12 x K8P: [(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate(Covalent)

K8P.1: 19 residues within 4Å: Chain A: D.40, M.59, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.97, A:V.122, A:K.165 Hydrogen bonds: A:D.40, A:D.40, A:E.121, A:E.121, A:V.122, A:G.169, A:G.230, A:G.251, A:S.252 Water bridges: A:G.229, A:G.229, A:G.253 K8P.5: 18 residues within 4Å: Chain B: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.97, B:V.122, B:K.165 Hydrogen bonds: B:D.40, B:D.40, B:E.121, B:E.121, B:V.122, B:G.169, B:G.230, B:G.251, B:S.252 Water bridges: B:G.229, B:G.253 K8P.9: 17 residues within 4Å: Chain C: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:K.97, C:V.122, C:K.165 Hydrogen bonds: C:D.40, C:D.40, C:K.97, C:E.121, C:V.122, C:G.169, C:G.230, C:G.251, C:S.252 Water bridges: C:G.229, C:V.231, C:V.231, C:V.231 K8P.12: 18 residues within 4Å: Chain D: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:K.97, D:V.122, D:K.165 Hydrogen bonds: D:D.40, D:D.40, D:K.97, D:V.122, D:E.167, D:G.169, D:G.230, D:G.251, D:S.252 Water bridges: D:V.231, D:V.231 K8P.15: 19 residues within 4Å: Chain E: D.40, M.59, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:K.97, E:V.122, E:K.165 Hydrogen bonds: E:D.40, E:D.40, E:E.121, E:E.121, E:V.122, E:K.165, E:G.169, E:G.230, E:G.251, E:S.252 Water bridges: E:G.229, E:G.229, E:G.253 K8P.19: 18 residues within 4Å: Chain F: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:K.97, F:V.122, F:K.165 Hydrogen bonds: F:D.40, F:D.40, F:E.121, F:E.121, F:V.122, F:K.165, F:G.169, F:G.230, F:G.251, F:S.252 Water bridges: F:G.229, F:G.253 K8P.23: 17 residues within 4Å: Chain G: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:K.97, G:V.122, G:K.165 Hydrogen bonds: G:D.40, G:D.40, G:K.97, G:E.121, G:V.122, G:G.169, G:G.230, G:G.251, G:S.252 Water bridges: G:G.229, G:V.231, G:V.231, G:V.231 K8P.26: 18 residues within 4Å: Chain H: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:K.97, H:V.122, H:K.165 Hydrogen bonds: H:D.40, H:D.40, H:K.97, H:V.122, H:E.167, H:G.169, H:G.230, H:G.251, H:S.252 Water bridges: H:V.231, H:V.231 K8P.29: 19 residues within 4Å: Chain I: D.40, M.59, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 15 PLIP interactions: 15 interactions with chain I Hydrophobic interactions: I:K.97, I:V.122, I:K.165 Hydrogen bonds: I:D.40, I:D.40, I:E.121, I:E.121, I:V.122, I:G.169, I:G.230, I:G.251, I:S.252 Water bridges: I:G.229, I:G.229, I:G.253 K8P.33: 18 residues within 4Å: Chain J: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:K.97, J:V.122, J:K.165 Hydrogen bonds: J:D.40, J:D.40, J:E.121, J:E.121, J:V.122, J:G.169, J:G.230, J:G.251, J:S.252 Water bridges: J:G.229, J:G.253 K8P.37: 17 residues within 4Å: Chain K: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:K.97, K:V.122, K:K.165 Hydrogen bonds: K:D.40, K:D.40, K:K.97, K:E.121, K:V.122, K:G.169, K:G.230, K:G.251, K:S.252 Water bridges: K:G.229, K:V.231, K:V.231, K:V.231 K8P.40: 18 residues within 4Å: Chain L: D.40, P.65, K.97, D.118, S.120, E.121, V.122, R.163, K.165, E.167, A.168, G.169, G.229, G.230, F.249, V.250, G.251, S.252 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:K.97, L:V.122, L:K.165 Hydrogen bonds: L:D.40, L:D.40, L:K.97, L:V.122, L:K.165, L:E.167, L:G.169, L:G.230, L:G.251, L:S.252 Water bridges: L:V.231, L:V.231

12 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.2: 10 residues within 4Å: Chain A: I.100, E.121, L.125, E.128, H.131, E.150, R.153, R.154 Chain D: K.203 Ligands: HG3.3 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:E.128, A:R.146 Water bridges: A:R.153, A:R.154, D:K.203, D:K.203 Salt bridges: A:H.131, A:H.131, A:R.153, A:R.154, D:K.203 RP5.6: 9 residues within 4Å: Chain B: I.100, E.121, L.125, E.128, H.131, R.153, R.154 Chain C: K.203 Ligands: HG3.7 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.146 Water bridges: B:R.153, C:K.203, C:K.203, C:K.203 Salt bridges: B:H.131, B:H.131, B:R.153, B:R.154, C:K.203 RP5.10: 11 residues within 4Å: Chain B: K.203 Chain C: I.100, E.121, L.125, E.128, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.11 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:E.128, C:R.146 Water bridges: C:E.121, C:E.150, C:R.153, B:T.200, B:K.203, B:K.203 Salt bridges: C:H.131, C:H.131, C:R.153, C:R.154, B:K.203 RP5.13: 10 residues within 4Å: Chain A: K.203 Chain D: I.100, E.121, L.125, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.14 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:E.128, D:R.146 Water bridges: D:E.121, D:E.121, D:E.121, D:H.131, D:H.131, D:R.153, D:E.157, A:T.200, A:K.203 Salt bridges: D:H.131, D:H.131, D:R.153, D:R.154, A:K.203 RP5.16: 10 residues within 4Å: Chain E: I.100, E.121, L.125, E.128, H.131, E.150, R.153, R.154 Chain H: K.203 Ligands: HG3.17 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain H Hydrogen bonds: E:E.128, E:R.146 Water bridges: E:R.153, E:R.154, H:K.203, H:K.203 Salt bridges: E:H.131, E:H.131, E:R.153, E:R.154, H:K.203 RP5.20: 9 residues within 4Å: Chain F: I.100, E.121, L.125, E.128, H.131, R.153, R.154 Chain G: K.203 Ligands: HG3.21 10 PLIP interactions: 4 interactions with chain G, 6 interactions with chain F Water bridges: G:K.203, G:K.203, G:K.203, F:R.153 Salt bridges: G:K.203, F:H.131, F:H.131, F:R.153, F:R.154 Hydrogen bonds: F:R.146 RP5.24: 11 residues within 4Å: Chain F: K.203 Chain G: I.100, E.121, L.125, E.128, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.25 13 PLIP interactions: 9 interactions with chain G, 4 interactions with chain F Hydrogen bonds: G:E.128, G:R.146 Water bridges: G:E.121, G:E.150, G:R.153, F:T.200, F:K.203, F:K.203 Salt bridges: G:H.131, G:H.131, G:R.153, G:R.154, F:K.203 RP5.27: 10 residues within 4Å: Chain E: K.203 Chain H: I.100, E.121, L.125, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.28 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain H Water bridges: E:T.200, E:K.203, H:E.121, H:E.121, H:E.121, H:H.131, H:H.131, H:R.153, H:E.157 Salt bridges: E:K.203, H:H.131, H:H.131, H:R.153, H:R.154 Hydrogen bonds: H:E.128, H:R.146 RP5.30: 10 residues within 4Å: Chain I: I.100, E.121, L.125, E.128, H.131, E.150, R.153, R.154 Chain L: K.203 Ligands: HG3.31 14 PLIP interactions: 9 interactions with chain I, 5 interactions with chain L Hydrogen bonds: I:E.128, I:R.146 Water bridges: I:D.129, I:R.153, I:R.154, L:K.203, L:K.203, L:K.203, L:K.203 Salt bridges: I:H.131, I:H.131, I:R.153, I:R.154, L:K.203 RP5.34: 9 residues within 4Å: Chain J: I.100, E.121, L.125, E.128, H.131, R.153, R.154 Chain K: K.203 Ligands: HG3.35 10 PLIP interactions: 4 interactions with chain K, 6 interactions with chain J Water bridges: K:K.203, K:K.203, K:K.203, J:R.153 Salt bridges: K:K.203, J:H.131, J:H.131, J:R.153, J:R.154 Hydrogen bonds: J:R.146 RP5.38: 11 residues within 4Å: Chain J: K.203 Chain K: I.100, E.121, L.125, E.128, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.39 13 PLIP interactions: 9 interactions with chain K, 4 interactions with chain J Hydrogen bonds: K:E.128, K:R.146 Water bridges: K:E.121, K:E.150, K:R.153, J:T.200, J:K.203, J:K.203 Salt bridges: K:H.131, K:H.131, K:R.153, K:R.154, J:K.203 RP5.41: 10 residues within 4Å: Chain I: K.203 Chain L: I.100, E.121, L.125, H.131, R.146, E.150, R.153, R.154 Ligands: HG3.42 16 PLIP interactions: 13 interactions with chain L, 3 interactions with chain I Hydrogen bonds: L:E.128, L:R.146 Water bridges: L:E.121, L:E.121, L:E.121, L:H.131, L:H.131, L:R.153, L:E.157, I:T.200, I:K.203 Salt bridges: L:H.131, L:H.131, L:R.153, L:R.154, I:K.203

12 x HG3: [(2~{R})-2,3,3-tris(oxidanyl)propyl] dihydrogen phosphate(Non-covalent)

HG3.3: 7 residues within 4Å: Chain A: E.121, H.131, E.150, R.153, R.154 Chain D: K.203 Ligands: RP5.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.131 Water bridges: A:R.146, A:R.154, D:K.203, D:K.203 Salt bridges: A:H.131, A:R.153, A:R.154, D:K.203 HG3.7: 6 residues within 4Å: Chain B: H.131, E.150, R.153, R.154 Chain C: K.203 Ligands: RP5.6 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Water bridges: B:R.146, B:R.146, B:R.146, B:R.154, C:K.203, C:K.203 Salt bridges: B:H.131, B:R.153, B:R.154, C:K.203 HG3.11: 8 residues within 4Å: Chain B: K.203 Chain C: I.100, E.121, H.131, E.150, R.153, R.154 Ligands: RP5.10 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.131, C:R.146, C:E.150 Water bridges: C:E.121, C:E.121, C:H.131, C:R.153, C:R.154, B:T.200, B:K.203 Salt bridges: C:H.131, C:R.153, C:R.154, B:K.203 HG3.14: 8 residues within 4Å: Chain A: K.203 Chain D: E.121, H.131, R.146, E.150, R.153, R.154 Ligands: RP5.13 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.131, D:E.150 Water bridges: D:E.121, D:E.121, D:E.121, D:H.131, D:H.131, D:H.131, D:R.146, D:R.146, D:R.146, D:R.154, D:E.157, A:T.200 Salt bridges: D:H.131, D:R.146, D:R.153, D:R.154, A:K.203 HG3.17: 7 residues within 4Å: Chain E: E.121, H.131, E.150, R.153, R.154 Chain H: K.203 Ligands: RP5.16 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain H Hydrogen bonds: E:H.131 Water bridges: E:R.146, E:R.154, H:K.203, H:K.203 Salt bridges: E:H.131, E:R.153, E:R.154, H:K.203 HG3.21: 6 residues within 4Å: Chain F: H.131, E.150, R.153, R.154 Chain G: K.203 Ligands: RP5.20 10 PLIP interactions: 3 interactions with chain G, 7 interactions with chain F Water bridges: G:K.203, G:K.203, F:R.146, F:R.146, F:R.146, F:R.154 Salt bridges: G:K.203, F:H.131, F:R.153, F:R.154 HG3.25: 8 residues within 4Å: Chain F: K.203 Chain G: I.100, E.121, H.131, E.150, R.153, R.154 Ligands: RP5.24 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:H.131, G:R.146, G:E.150 Water bridges: G:E.121, G:E.121, G:H.131, G:R.153, G:R.154, F:T.200, F:K.203 Salt bridges: G:H.131, G:R.153, G:R.154, F:K.203 HG3.28: 8 residues within 4Å: Chain E: K.203 Chain H: E.121, H.131, R.146, E.150, R.153, R.154 Ligands: RP5.27 19 PLIP interactions: 2 interactions with chain E, 17 interactions with chain H Water bridges: E:T.200, H:E.121, H:E.121, H:E.121, H:H.131, H:H.131, H:H.131, H:R.146, H:R.146, H:R.146, H:R.154, H:E.157 Salt bridges: E:K.203, H:H.131, H:R.146, H:R.153, H:R.154 Hydrogen bonds: H:H.131, H:E.150 HG3.31: 7 residues within 4Å: Chain I: E.121, H.131, E.150, R.153, R.154 Chain L: K.203 Ligands: RP5.30 11 PLIP interactions: 4 interactions with chain L, 7 interactions with chain I Water bridges: L:K.203, L:K.203, L:K.203, I:R.146, I:R.154 Salt bridges: L:K.203, I:H.131, I:R.153, I:R.154 Hydrogen bonds: I:H.131, I:E.150 HG3.35: 6 residues within 4Å: Chain J: H.131, E.150, R.153, R.154 Chain K: K.203 Ligands: RP5.34 10 PLIP interactions: 3 interactions with chain K, 7 interactions with chain J Water bridges: K:K.203, K:K.203, J:R.146, J:R.146, J:R.146, J:R.154 Salt bridges: K:K.203, J:H.131, J:R.153, J:R.154 HG3.39: 8 residues within 4Å: Chain J: K.203 Chain K: I.100, E.121, H.131, E.150, R.153, R.154 Ligands: RP5.38 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain J Hydrogen bonds: K:H.131, K:R.146, K:E.150 Water bridges: K:E.121, K:E.121, K:H.131, K:R.153, K:R.154, J:T.200, J:K.203 Salt bridges: K:H.131, K:R.153, K:R.154, J:K.203 HG3.42: 8 residues within 4Å: Chain I: K.203 Chain L: E.121, H.131, R.146, E.150, R.153, R.154 Ligands: RP5.41 19 PLIP interactions: 17 interactions with chain L, 2 interactions with chain I Hydrogen bonds: L:H.131, L:E.150 Water bridges: L:E.121, L:E.121, L:E.121, L:H.131, L:H.131, L:H.131, L:R.146, L:R.146, L:R.146, L:R.154, L:E.157, I:T.200 Salt bridges: L:H.131, L:R.146, L:R.153, L:R.154, I:K.203

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.196 Chain C: Q.242 Chain D: F.103, N.136 8 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 5 interactions with chain D Water bridges: A:D.196, A:D.196, C:Q.242, D:Q.107, D:Q.107, D:N.133, D:N.133 Hydrogen bonds: D:N.136 GOL.8: 4 residues within 4Å: Chain B: D.196 Chain C: F.103, N.136 Chain L: Q.242 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain L, 3 interactions with chain C Water bridges: B:D.194, B:D.196, C:N.133, C:N.133 Hydrogen bonds: L:Q.242, C:N.136 GOL.18: 4 residues within 4Å: Chain E: D.196 Chain G: Q.242 Chain H: F.103, N.136 8 PLIP interactions: 5 interactions with chain H, 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: H:N.136 Water bridges: H:Q.107, H:Q.107, H:N.133, H:N.133, E:D.196, E:D.196, G:Q.242 GOL.22: 4 residues within 4Å: Chain D: Q.242 Chain F: D.196 Chain G: F.103, N.136 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F, 3 interactions with chain G Hydrogen bonds: D:Q.242, G:N.136 Water bridges: F:D.194, F:D.196, G:N.133, G:N.133 GOL.32: 4 residues within 4Å: Chain I: D.196 Chain K: Q.242 Chain L: F.103, N.136 8 PLIP interactions: 5 interactions with chain L, 2 interactions with chain I, 1 interactions with chain K Hydrogen bonds: L:N.136 Water bridges: L:Q.107, L:Q.107, L:N.133, L:N.133, I:D.196, I:D.196, K:Q.242 GOL.36: 4 residues within 4Å: Chain H: Q.242 Chain J: D.196 Chain K: F.103, N.136 6 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H, 3 interactions with chain K Water bridges: J:D.194, J:D.196, K:N.133, K:N.133 Hydrogen bonds: H:Q.242, K:N.136

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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