SMTL ID : 8s2x.1

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

12 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 6 residues within 4Å: Chain A: H.131, E.150, R.153, R.154, K.165 Chain D: K.203 16 PLIP interactions: 2 interactions with chain D, 14 interactions with chain A Salt bridges: D:K.203, D:K.203, A:H.131, A:R.146, A:R.153, A:R.153, A:R.154, A:K.165 Hydrogen bonds: A:R.153 Water bridges: A:D.129, A:H.131, A:H.131, A:E.150, A:R.154, A:R.154, A:K.165 CIT.3: 7 residues within 4Å: Chain B: H.131, R.146, E.150, R.153, R.154, K.165 Chain C: K.203 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.146 Salt bridges: B:H.131, B:H.131, B:R.153, B:R.153, B:R.154, B:K.165, C:K.203, C:K.203 CIT.5: 7 residues within 4Å: Chain B: K.203 Chain C: H.131, R.146, E.150, R.153, R.154, K.165 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.153 Water bridges: C:R.154, C:K.165 Salt bridges: C:H.131, C:R.146, C:R.153, C:R.154, C:K.165, B:K.203, B:K.203 CIT.7: 6 residues within 4Å: Chain A: K.203 Chain D: H.131, E.150, R.153, R.154, K.165 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.150 Water bridges: D:R.154, D:R.154, D:K.165 Salt bridges: D:H.131, D:R.153, D:R.153, D:R.154, D:K.165, A:K.203, A:K.203 CIT.9: 6 residues within 4Å: Chain E: H.131, E.150, R.153, R.154, K.165 Chain H: K.203 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:R.153 Water bridges: E:D.129, E:H.131, E:H.131, E:E.150, E:R.154, E:R.154, E:K.165 Salt bridges: E:H.131, E:R.146, E:R.153, E:R.153, E:R.154, E:K.165, H:K.203, H:K.203 CIT.11: 7 residues within 4Å: Chain F: H.131, R.146, E.150, R.153, R.154, K.165 Chain G: K.203 9 PLIP interactions: 2 interactions with chain G, 7 interactions with chain F Salt bridges: G:K.203, G:K.203, F:H.131, F:H.131, F:R.153, F:R.153, F:R.154, F:K.165 Hydrogen bonds: F:R.146 CIT.13: 7 residues within 4Å: Chain F: K.203 Chain G: H.131, R.146, E.150, R.153, R.154, K.165 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:R.153 Water bridges: G:R.154, G:K.165 Salt bridges: G:H.131, G:R.146, G:R.153, G:R.154, G:K.165, F:K.203, F:K.203 CIT.15: 6 residues within 4Å: Chain E: K.203 Chain H: H.131, E.150, R.153, R.154, K.165 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:E.150 Water bridges: H:R.154, H:R.154, H:K.165 Salt bridges: H:H.131, H:R.153, H:R.153, H:R.154, H:K.165, E:K.203, E:K.203 CIT.17: 6 residues within 4Å: Chain I: H.131, E.150, R.153, R.154, K.165 Chain L: K.203 16 PLIP interactions: 14 interactions with chain I, 2 interactions with chain L Hydrogen bonds: I:R.153 Water bridges: I:D.129, I:H.131, I:H.131, I:E.150, I:R.154, I:R.154, I:K.165 Salt bridges: I:H.131, I:R.146, I:R.153, I:R.153, I:R.154, I:K.165, L:K.203, L:K.203 CIT.19: 7 residues within 4Å: Chain J: H.131, R.146, E.150, R.153, R.154, K.165 Chain K: K.203 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:R.146 Salt bridges: J:H.131, J:H.131, J:R.153, J:R.153, J:R.154, J:K.165, K:K.203, K:K.203 CIT.21: 7 residues within 4Å: Chain J: K.203 Chain K: H.131, R.146, E.150, R.153, R.154, K.165 10 PLIP interactions: 8 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:R.153 Water bridges: K:R.154, K:K.165 Salt bridges: K:H.131, K:R.146, K:R.153, K:R.154, K:K.165, J:K.203, J:K.203 CIT.23: 6 residues within 4Å: Chain I: K.203 Chain L: H.131, E.150, R.153, R.154, K.165 11 PLIP interactions: 9 interactions with chain L, 2 interactions with chain I Hydrogen bonds: L:E.150 Water bridges: L:R.154, L:R.154, L:K.165 Salt bridges: L:H.131, L:R.153, L:R.153, L:R.154, L:K.165, I:K.203, I:K.203

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

PO4.2: 5 residues within 4Å: Chain A: A.168, G.169, G.229, G.230, G.251 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.169, A:G.229, A:G.230, A:G.251 Water bridges: A:V.231, A:V.231 PO4.4: 6 residues within 4Å: Chain B: A.168, G.169, G.229, G.230, V.250, G.251 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.169, B:G.229, B:G.230, B:G.251 Water bridges: B:V.231, B:F.249 PO4.6: 6 residues within 4Å: Chain C: A.168, G.169, T.170, G.229, G.230, G.251 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.169, C:T.170, C:G.230, C:G.251 Water bridges: C:G.229 PO4.8: 8 residues within 4Å: Chain D: A.168, G.169, T.170, G.171, G.229, G.230, V.231, G.251 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.169, D:T.170, D:G.171, D:G.229, D:G.230, D:G.251 Water bridges: D:V.231, D:V.231 PO4.10: 5 residues within 4Å: Chain E: A.168, G.169, G.229, G.230, G.251 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.169, E:G.229, E:G.230, E:G.251 Water bridges: E:V.231, E:V.231 PO4.12: 6 residues within 4Å: Chain F: A.168, G.169, G.229, G.230, V.250, G.251 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.169, F:G.229, F:G.230, F:G.251 Water bridges: F:V.231, F:F.249 PO4.14: 6 residues within 4Å: Chain G: A.168, G.169, T.170, G.229, G.230, G.251 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:G.169, G:T.170, G:G.230, G:G.251 Water bridges: G:G.229 PO4.16: 8 residues within 4Å: Chain H: A.168, G.169, T.170, G.171, G.229, G.230, V.231, G.251 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:G.169, H:T.170, H:G.171, H:G.229, H:G.230, H:G.251 Water bridges: H:V.231, H:V.231 PO4.18: 5 residues within 4Å: Chain I: A.168, G.169, G.229, G.230, G.251 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:G.169, I:G.229, I:G.230, I:G.251 Water bridges: I:V.231, I:V.231 PO4.20: 6 residues within 4Å: Chain J: A.168, G.169, G.229, G.230, V.250, G.251 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:G.169, J:G.229, J:G.230, J:G.251 Water bridges: J:V.231, J:F.249 PO4.22: 6 residues within 4Å: Chain K: A.168, G.169, T.170, G.229, G.230, G.251 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:G.169, K:T.170, K:G.230, K:G.251 Water bridges: K:G.229 PO4.24: 8 residues within 4Å: Chain L: A.168, G.169, T.170, G.171, G.229, G.230, V.231, G.251 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:G.169, L:T.170, L:G.171, L:G.229, L:G.230, L:G.251 Water bridges: L:V.231, L:V.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stubbs, J. et al., Droplet microfluidics for time-resolved serial crystallography. Iucrj (2024)

Release Date

2024-02-28

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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