SMTL ID : 8wcn.1

Cryo-EM structure of PAO1-ImcA with GMPCPP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.1: 16 residues within 4Å: Chain A: D.286, V.287, D.288, D.289, F.290, K.291, N.294, L.306, R.326, G.329, E.330, K.401, R.405 Chain B: R.259, Y.390 Ligands: MG.3 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.288, A:D.289, A:F.290, A:K.291, A:K.291, A:K.291, A:N.294, A:R.326, A:E.330, A:R.405, B:R.259, B:R.259, B:Y.390 Salt bridges: A:K.401 pi-Cation interactions: B:R.259 G2P.2: 9 residues within 4Å: Chain A: R.44, Y.228, Y.232 Chain B: F.59, N.63, M.66, Q.234, Q.237, R.241 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.234, B:Q.237, B:R.241, B:R.241 G2P.4: 15 residues within 4Å: Chain A: R.259, Y.390 Chain B: D.286, V.287, D.288, D.289, F.290, K.291, N.294, D.303, R.326, G.329, E.330, K.401 Ligands: MG.6 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.289, B:F.290, B:K.291, B:K.291, B:R.326, B:R.326, A:R.259, A:R.259, A:Y.390 Salt bridges: B:K.291, B:D.303, B:K.401 pi-Cation interactions: A:R.259 G2P.5: 9 residues within 4Å: Chain A: F.59, N.63, M.66, Q.67, Q.234, R.241 Chain B: R.44, Y.228, Y.232 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.44, B:Y.232, A:Q.67, A:Q.234, A:R.241, A:R.241

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.286, V.287, E.330 Ligands: G2P.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.287, A:E.330 MG.6: 4 residues within 4Å: Chain B: D.286, V.287, E.330 Ligands: G2P.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.286, B:V.287, B:E.330, B:E.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, X. et al., A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa. Nat Commun (2024)

Release Date

2024-03-13

Peptides

Diguanylate cyclase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Diguanylate cyclase