SMTL ID : 6hvl.1 (1 other biounit)

CdaA complex with c-di-AMP and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-covalent)

2BA.1: 19 residues within 4Å: Chain A: L.36, D.76, G.77, S.91, Y.92, L.93, L.95, G.106, T.107, R.108, A.111, E.128, E.129 Chain B: D.76, L.95, T.107 Ligands: CO.2, 2BA.4, CO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.76, A:G.77, A:L.93, A:L.93, A:T.107, A:R.108 2BA.4: 19 residues within 4Å: Chain A: D.76, L.95, T.107 Chain B: L.36, D.76, G.77, S.91, Y.92, L.93, L.95, G.106, T.107, R.108, A.111, E.128, E.129 Ligands: 2BA.1, CO.2, CO.5 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.107, B:D.76, B:G.77, B:L.93, B:L.93, B:T.107, B:T.107, B:R.108

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 5 residues within 4Å: Chain A: E.129 Chain B: H.75, D.76 Ligands: 2BA.1, 2BA.4 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: A:E.129, B:D.76, B:D.76, 2BA.1 CO.5: 5 residues within 4Å: Chain A: H.75, D.76 Chain B: E.129 Ligands: 2BA.1, 2BA.4 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:E.129, A:D.76, A:D.76, 2BA.4

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: D.76, A.90, Y.92 Chain B: L.105, G.106, T.107, R.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.105, B:L.105 Salt bridges: B:R.110 PO4.6: 7 residues within 4Å: Chain A: L.105, G.106, T.107, R.110 Chain B: D.76, A.90, Y.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.105, A:L.105 Salt bridges: A:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heidemann, J.L. et al., Crystal structures of the c-di-AMP-synthesizing enzyme CdaA. J.Biol.Chem. (2019)

Release Date

2019-06-05

Peptides

Diadenylate cyclase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diadenylate cyclase

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