SMTL ID : 5zk6.1

Crystal structure of RimK complexed with RpsF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.1: 18 residues within 4Å: Chain A: V.139, K.141, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, R.216, L.250, M.259, E.260 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.141, A:E.178, A:I.180, A:R.203, A:S.212, A:N.213, A:R.216, A:E.260 Salt bridges: A:K.141 ADP.3: 18 residues within 4Å: Chain B: V.139, K.141, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, R.216, L.250, M.259, E.260 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.141, B:E.178, B:I.180, B:R.203, B:S.212, B:N.213, B:R.216, B:E.260 Salt bridges: B:K.141 ADP.5: 18 residues within 4Å: Chain C: V.139, K.141, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, R.216, L.250, M.259, E.260 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.141, C:E.178, C:I.180, C:D.187, C:R.203, C:S.212, C:N.213, C:R.216, C:E.260 Salt bridges: C:K.141 ADP.7: 18 residues within 4Å: Chain D: V.139, K.141, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, R.216, L.250, M.259, E.260 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.141, D:E.178, D:I.180, D:D.187, D:R.203, D:S.212, D:N.213, D:R.216, D:E.260 Salt bridges: D:K.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.213, D.248, E.260 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.260 MG.4: 4 residues within 4Å: Chain B: N.213, D.248, E.260 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.260 MG.6: 4 residues within 4Å: Chain C: N.213, D.248, E.260 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.260 MG.8: 4 residues within 4Å: Chain D: N.213, D.248, E.260 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohnuki, J. et al., Molecular dynamics prediction of substrate recognition by poly-alpha-L-glutamate synthetase. To Be Published

Release Date

2019-03-27

Peptides

Ribosomal protein S6--L-glutamate ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Ribosomal protein S6--L-glutamate ligase

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