SMTL ID : 5zct.1 (1 other biounit)

The crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05 angstrom resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)(Non-covalent)

ANP.1: 23 residues within 4Å: Chain A: K.100, V.139, K.141, G.145, T.146, Q.147, G.148, I.149, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, L.250, M.259, E.260 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.100, A:K.141, A:Q.147, A:I.149, A:E.178, A:I.180, A:R.203, A:S.212, A:S.212, A:N.213, A:N.213 Water bridges: A:K.100, A:K.100, A:K.100, A:K.141, A:G.145, A:T.146, A:R.189, A:D.248, A:M.259, A:E.260 Salt bridges: A:K.141 ANP.6: 18 residues within 4Å: Chain B: K.100, 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, L.250, M.259, E.260 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.100, B:K.141, B:Q.177, B:I.180, B:R.203, B:S.212, B:S.212, B:N.213 Salt bridges: B:K.141 ANP.9: 22 residues within 4Å: Chain C: K.100, V.139, K.141, G.145, T.146, Q.147, G.148, V.151, Q.177, E.178, Y.179, I.180, D.187, R.203, F.210, R.211, S.212, N.213, L.250, M.259, E.260 Ligands: MG.10 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:K.100, C:K.100, C:K.141, C:G.148, C:Q.177, C:I.180, C:R.203, C:S.212, C:S.212, C:N.213, C:E.260, C:E.260 Water bridges: C:K.100, C:K.100, C:K.141, C:Q.147, C:Q.147, C:R.189, C:N.213, C:M.259 Salt bridges: C:K.141 ANP.14: 18 residues within 4Å: Chain D: K.100, 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, L.250, M.259, E.260 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:K.100, D:K.100, D:K.100, D:K.141, D:Q.177, D:I.180, D:S.212, D:S.212, D:N.213, D:N.213, D:E.260 Water bridges: D:G.185, D:R.203 Salt bridges: D:K.141

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: R.189, D.248, E.260 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.260 MG.10: 3 residues within 4Å: Chain C: N.213 Ligands: ANP.9, SO4.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: N.213, E.260 Ligands: ANP.14 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.260, D:E.260, H2O.19, H2O.20

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.284, R.288 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.284, A:R.284 Salt bridges: A:R.284, A:R.288 SO4.4: 5 residues within 4Å: Chain A: Q.147, R.189, R.203, N.213, L.214 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.213, A:L.214 Water bridges: A:Q.147, A:R.189, A:R.189, A:R.189, A:R.189, A:D.248 Salt bridges: A:R.189, A:R.203 SO4.5: 3 residues within 4Å: Chain A: R.96, R.102 Chain B: V.92 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:R.78, B:R.78, A:R.109 Salt bridges: A:R.96, A:R.102, A:R.109 SO4.8: 3 residues within 4Å: Chain B: R.96, R.102, R.109 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.109 Salt bridges: B:R.96, B:R.102 Water bridges: A:R.78 SO4.11: 6 residues within 4Å: Chain C: Q.147, R.189, R.203, N.213, L.214 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.213, C:L.214 Water bridges: C:Q.147, C:R.189, C:R.189, C:N.213, C:D.248 Salt bridges: C:R.189, C:R.203 SO4.12: 5 residues within 4Å: Chain C: R.96, R.102, L.106, R.109 Chain D: V.92 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.109 Salt bridges: C:R.96, C:R.102, C:R.109 SO4.13: 2 residues within 4Å: Chain C: R.284, R.288 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.284 Salt bridges: C:R.284, C:R.288 SO4.16: 3 residues within 4Å: Chain C: V.92 Chain D: R.96, R.102 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.96, D:R.102 Water bridges: C:R.78, C:S.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arimura, Y. et al., Structural polymorphism of the Escherichia coli poly-alpha-L-glutamate synthetase RimK. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-07-25

Peptides

Ribosomal protein S6--L-glutamate ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribosomal protein S6--L-glutamate ligase

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