SMTL ID : 3gfz.1

Klebsiella pneumoniae BlrP1 pH 6 manganese/cy-diGMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 23 residues within 4Å: Chain A: F.179, Q.182, E.196, L.198, I.199, R.200, P.207, F.211, D.223, K.227, N.247, L.249, D.310, D.311, E.367, G.368, V.369, E.370, G.388, F.389, P.394 Ligands: MN.2, MN.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.182, A:I.199, A:K.227, A:K.227, A:N.247, A:L.249, A:E.370, A:F.389 Water bridges: A:G.368 Salt bridges: A:R.200, A:D.223, A:E.370 pi-Stacking: A:F.389, A:F.389 C2E.5: 23 residues within 4Å: Chain B: F.179, Q.182, E.196, L.198, I.199, R.200, P.207, F.211, D.223, K.227, N.247, L.249, D.310, D.311, E.367, G.368, V.369, E.370, G.388, F.389, P.394 Ligands: MN.6, MN.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.182, B:I.199, B:K.227, B:K.227, B:N.247, B:L.249, B:E.370, B:F.389 Water bridges: B:D.310 Salt bridges: B:R.200, B:D.223, B:E.370 pi-Stacking: B:F.389, B:F.389

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: E.196, N.247, E.280, D.310 Ligands: C2E.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.196, A:E.280, A:D.310, C2E.1, H2O.8 MN.3: 4 residues within 4Å: Chain A: D.310, D.311, E.367 Ligands: C2E.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.310, A:D.311, A:E.367, C2E.1, H2O.8 MN.6: 5 residues within 4Å: Chain B: E.196, N.247, E.280, D.310 Ligands: C2E.5 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.196, B:E.280, B:D.310, C2E.5, H2O.14 MN.7: 4 residues within 4Å: Chain B: D.310, D.311, E.367 Ligands: C2E.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.310, B:D.311, B:E.367, B:E.367, C2E.5

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 16 residues within 4Å: Chain A: Y.15, L.31, R.34, A.35, K.38, N.39, F.55, Q.57, L.59, L.69, E.72, I.73, D.76, R.78, H.79, M.100 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.31, A:L.31, A:F.55, A:R.78 Hydrogen bonds: A:K.38, A:N.39, A:N.39, A:Q.57, A:D.76, A:D.76, A:R.78 Salt bridges: A:R.34, A:K.38 FMN.8: 17 residues within 4Å: Chain B: Y.15, L.31, R.34, A.35, K.38, N.39, L.48, F.55, Q.57, L.59, L.69, E.72, I.73, D.76, R.78, H.79, M.100 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.31, B:L.48, B:F.55, B:R.78 Hydrogen bonds: B:K.38, B:N.39, B:N.39, B:Q.57, B:D.76, B:D.76, B:R.78 Salt bridges: B:R.34, B:K.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barends, T.R. et al., Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature (2009)

Release Date

2009-06-23

Peptides

Klebsiella pneumoniae BlrP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Klebsiella pneumoniae BlrP1

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