SMTL ID : 7wx3.1

GK domain of Drosophila P5CS filament with glutamate, ATP, and NADPH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

4 x RGP: GAMMA-GLUTAMYL PHOSPHATE(Covalent)

RGP.1: 13 residues within 4Å: Chain A: K.62, S.65, S.103, G.104, A.105, V.106, N.204, T.205, D.207, M.213, N.233 Ligands: ADP.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.233 Hydrogen bonds: A:S.65, A:S.103, A:G.104, A:A.105, A:V.106, A:N.204 Salt bridges: A:K.62 RGP.4: 13 residues within 4Å: Chain C: K.62, S.65, S.103, G.104, A.105, V.106, N.204, T.205, D.207, M.213, N.233 Ligands: ADP.5, MG.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:N.233 Hydrogen bonds: C:S.65, C:S.103, C:G.104, C:A.105, C:V.106, C:N.204 Salt bridges: C:K.62 RGP.7: 13 residues within 4Å: Chain E: K.62, S.65, S.103, G.104, A.105, V.106, N.204, T.205, D.207, M.213, N.233 Ligands: ADP.8, MG.9 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:N.233 Hydrogen bonds: E:S.65, E:S.103, E:G.104, E:A.105, E:V.106, E:N.204, E:N.204, E:T.205 Salt bridges: E:K.62 RGP.10: 13 residues within 4Å: Chain G: K.62, S.65, S.103, G.104, A.105, V.106, N.204, T.205, D.207, M.213, N.233 Ligands: ADP.11, MG.12 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:N.233 Hydrogen bonds: G:S.65, G:S.103, G:G.104, G:A.105, G:V.106, G:N.204, G:N.204, G:T.205 Salt bridges: G:K.62

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 10 residues within 4Å: Chain A: G.64, S.65, A.66, D.254, V.255, Y.259, M.295, K.298 Ligands: RGP.1, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.65, A:A.66, A:D.254, A:Y.259, A:Y.259 Salt bridges: A:K.62, A:K.298, A:K.298 ADP.5: 10 residues within 4Å: Chain C: G.64, S.65, A.66, D.254, V.255, Y.259, M.295, K.298 Ligands: RGP.4, MG.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.65, C:A.66, C:D.254, C:Y.259, C:Y.259 Salt bridges: C:K.62, C:K.298, C:K.298 ADP.8: 10 residues within 4Å: Chain E: G.64, S.65, A.66, D.254, V.255, Y.259, M.295, K.298 Ligands: RGP.7, MG.9 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.65, E:A.66, E:D.254, E:Y.259, E:Y.259 Salt bridges: E:K.62, E:K.298, E:K.298 ADP.11: 10 residues within 4Å: Chain G: G.64, S.65, A.66, D.254, V.255, Y.259, M.295, K.298 Ligands: RGP.10, MG.12 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.65, G:A.66, G:D.254, G:Y.259, G:Y.259 Salt bridges: G:K.62, G:K.298, G:K.298

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.232 Ligands: RGP.1, ADP.2 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: D.232 Ligands: RGP.4, ADP.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: D.232 Ligands: RGP.7, ADP.8 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain G: D.232 Ligands: RGP.10, ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, J. et al., Structural basis of dynamic P5CS filaments. Elife (2022)

Release Date

2022-04-06

Peptides

Delta-1-pyrroline-5-carboxylate synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
B

D
F

E
C

F
G

G
D

H
H

Delta-1-pyrroline-5-carboxylate synthase

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