SMTL ID : 5l9n.1

Structure of uridylylated GlnB from Escherichia coli bound to ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: I.7, G.35, F.36, K.58, K.85, I.86, G.87, D.88, G.89, K.90, F.92 Chain B: G.27, M.28, T.29, E.62, I.63, V.64, R.101, I.102, R.103 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:G.87, A:D.88, A:G.89, B:M.28, B:T.29, B:V.64, B:V.64, B:I.102, B:R.103 Salt bridges: A:K.90, A:K.90, B:R.101, B:R.101, B:R.103 pi-Stacking: A:F.92 ATP.3: 20 residues within 4Å: Chain B: I.7, G.35, F.36, K.58, K.85, I.86, G.87, D.88, G.89, K.90, F.92 Chain C: G.27, M.28, T.29, E.62, I.63, V.64, R.101, I.102, R.103 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:G.87, B:D.88, B:G.89, C:M.28, C:T.29, C:V.64, C:V.64, C:I.102, C:R.103 Salt bridges: B:K.90, B:K.90, C:R.101, C:R.101, C:R.103 pi-Stacking: B:F.92 ATP.5: 20 residues within 4Å: Chain A: G.27, M.28, T.29, E.62, I.63, V.64, R.101, I.102, R.103 Chain C: I.7, G.35, F.36, K.58, K.85, I.86, G.87, D.88, G.89, K.90, F.92 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:M.28, A:V.64, A:V.64, A:I.102, A:R.103, C:G.87, C:D.88, C:G.89 Salt bridges: A:R.101, A:R.101, A:R.103, C:K.90, C:K.90 pi-Stacking: C:F.92

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: F.11, D.14, D.15 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.11, A:D.14, A:D.15 MG.4: 3 residues within 4Å: Chain B: F.11, D.14, D.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:F.11, B:D.14, B:D.15 MG.6: 3 residues within 4Å: Chain C: F.11, D.14, D.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:F.11, C:D.14, C:D.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palanca, C. et al., Effects of T-loop modification on the PII-signalling protein: structure of uridylylated Escherichia coli GlnB bound to ATP. Environ Microbiol Rep (2017)

Release Date

2017-04-05

Peptides

Nitrogen regulatory protein P-II 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrogen regulatory protein P-II 1

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