SMTL ID : 8j0f.1

GK tetramer with adjacent hooks at reaction state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: K.20, G.22, T.23, A.24, D.197, V.198, G.200, Y.202, G.204, P.206, F.228, G.238, M.239, K.242 Ligands: RGP.2, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.23, A:T.23, A:A.24, A:D.197, A:Y.202, A:Y.202 Salt bridges: A:K.20, A:K.242, A:K.242 ADP.4: 16 residues within 4Å: Chain C: K.20, G.22, T.23, A.24, D.197, V.198, G.200, Y.202, G.204, P.206, F.228, G.238, M.239, K.242 Ligands: RGP.5, MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.23, C:T.23, C:A.24, C:D.197, C:Y.202, C:Y.202 Salt bridges: C:K.20, C:K.242, C:K.242 ADP.7: 16 residues within 4Å: Chain E: K.20, G.22, T.23, A.24, D.197, V.198, G.200, Y.202, G.204, P.206, F.228, G.238, M.239, K.242 Ligands: RGP.8, MG.9 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:A.24, E:D.197, E:Y.202, E:Y.202 Salt bridges: E:K.20, E:K.242, E:K.242 ADP.10: 16 residues within 4Å: Chain G: K.20, G.22, T.23, A.24, D.197, V.198, G.200, Y.202, G.204, P.206, F.228, G.238, M.239, K.242 Ligands: RGP.11, MG.12 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:A.24, G:D.197, G:Y.202, G:Y.202 Salt bridges: G:K.20, G:K.242, G:K.242

4 x RGP: GAMMA-GLUTAMYL PHOSPHATE(Non-covalent)

RGP.2: 13 residues within 4Å: Chain A: K.20, G.22, T.23, S.60, G.61, A.62, V.63, D.157, N.176, D.177, R.236 Ligands: ADP.1, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.23, A:T.23, A:S.60, A:G.61, A:A.62, A:V.63, A:D.157 Salt bridges: A:K.20, A:R.236 RGP.5: 13 residues within 4Å: Chain C: K.20, G.22, T.23, S.60, G.61, A.62, V.63, D.157, N.176, D.177, R.236 Ligands: ADP.4, MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.23, C:T.23, C:S.60, C:G.61, C:A.62, C:V.63, C:D.157 Salt bridges: C:K.20, C:R.236 RGP.8: 13 residues within 4Å: Chain E: K.20, G.22, T.23, S.60, G.61, A.62, V.63, D.157, N.176, D.177, R.236 Ligands: ADP.7, MG.9 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:T.23, E:S.60, E:G.61, E:A.62, E:V.63, E:D.157, E:R.236 Salt bridges: E:K.20, E:R.236 RGP.11: 13 residues within 4Å: Chain G: K.20, G.22, T.23, S.60, G.61, A.62, V.63, D.157, N.176, D.177, R.236 Ligands: ADP.10, MG.12 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:T.23, G:S.60, G:G.61, G:A.62, G:V.63, G:D.157, G:R.236 Salt bridges: G:K.20, G:R.236

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.177, R.236, G.237, G.238 Ligands: ADP.1, RGP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:R.236 MG.6: 6 residues within 4Å: Chain C: D.177, R.236, G.237, G.238 Ligands: ADP.4, RGP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:R.236 MG.9: 6 residues within 4Å: Chain E: D.177, R.236, G.237, G.238 Ligands: ADP.7, RGP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:R.236 MG.12: 6 residues within 4Å: Chain G: D.177, R.236, G.237, G.238 Ligands: ADP.10, RGP.11 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, T. et al., GK tetramer with adjacent hooks at reaction state. To Be Published

Release Date

2024-04-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

C
A

D
E

E
B

F
G

G
D

H
H

Delta-1-pyrroline-5-carboxylate synthase B

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