SMTL ID : 7qys.1 (3 other biounits)

Crystal structure of RimK from Pseudomonas syringae DC3000

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: V.139, K.141, V.151, Q.177, E.178, Y.179, I.180, D.187, F.210, S.212, L.250, M.259, E.260 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.141, A:E.178, A:I.180, A:D.187, A:S.212 Salt bridges: A:K.141 ADP.2: 13 residues within 4Å: Chain B: V.139, Q.177, E.178, Y.179, I.180, G.185, A.186, D.187, R.203, D.248, L.250, M.259, E.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.178, B:I.180, B:A.186 ADP.3: 10 residues within 4Å: Chain C: V.139, V.151, Q.177, E.178, Y.179, I.180, D.187, L.250, M.259, E.260 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.178, C:I.180, C:D.187, C:D.187 ADP.4: 13 residues within 4Å: Chain D: V.139, K.141, Q.177, E.178, Y.179, I.180, D.187, F.210, S.212, N.213, L.250, M.259, E.260 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.141, D:E.178, D:I.180, D:S.212, D:S.212, D:N.213, D:E.260 Salt bridges: D:K.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, C.M.A. et al., Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK. Proteins (2023)

Release Date

2022-10-05

Peptides

Probable alpha-L-glutamate ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable alpha-L-glutamate ligase

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