SMTL ID : 8fxi.1

Cryo-EM structure of Stanieria sp. CphA2 in complex with ADPCP and 4x(beta-Asp-Arg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

2 x 7ID- 7ID- 7ID: 4x(beta-Asp-Arg)(Non-covalent)

7ID-7ID-7ID.1: 17 residues within 4Å: Chain C: G.161, P.162, T.163, V.164, T.202, S.211, D.212, T.215, R.308, N.451, A.452, A.453, P.454, G.455 Chain D: H.208, I.209, D.212 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.162, C:T.202, C:N.451, C:A.452, C:A.453 Hydrogen bonds: C:T.202, C:S.211, C:T.215, C:R.308, C:R.308, C:A.452, C:A.453, C:A.453, C:A.453, C:A.453, D:I.209 Salt bridges: C:D.212, D:D.212 7ID-7ID-7ID.2: 17 residues within 4Å: Chain C: H.208, I.209, D.212 Chain D: G.161, P.162, T.163, V.164, T.202, S.211, D.212, T.215, R.308, N.451, A.452, A.453, P.454, G.455 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.162, D:T.202, D:N.451, D:A.452, D:A.453 Hydrogen bonds: D:T.202, D:S.211, D:T.215, D:R.308, D:R.308, D:A.452, D:A.453, D:A.453, D:A.453, D:A.453, C:I.209 Salt bridges: D:D.212, C:D.212

1 x YHZ: 1-[(4-aminopyrimidin-5-yl)amino]-2,5-anhydro-1-deoxy-6-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]-D-allitol(Non-covalent)

YHZ.3: 10 residues within 4Å: Chain C: G.261, H.262, I.265, I.302, V.391, I.432, I.448, E.449 Ligands: MG.4, MG.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.298

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain C: I.448, E.449 Ligands: YHZ.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: E.449 Ligands: YHZ.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.449 MG.7: 3 residues within 4Å: Chain D: I.448, E.449 Ligands: ACP.6 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: E.449 Ligands: ACP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.449

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.6: 10 residues within 4Å: Chain D: G.261, H.262, I.265, I.302, V.391, I.432, I.448, E.449 Ligands: MG.7, MG.8 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Markus, L.M.D. et al., Structure and function of a hexameric cyanophycin synthetase 2. Protein Sci. (2023)

Release Date

2023-06-14

Peptides

RimK domain-containing protein ATP-grasp: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

RimK domain-containing protein ATP-grasp

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