SMTL ID : 4rle.1

Crystal structure of the c-di-AMP binding PII-like protein DarA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 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: 21 residues within 4Å: Chain A: T.29, N.32, F.33, R.34, V.35, T.36, M.53, I.54, G.55 Chain C: V.15, G.42, G.43, F.44, L.45, N.49, V.99, E.100, V.101, G.102, T.105, F.107 25 PLIP interactions: 16 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:G.42, C:G.43, C:F.44, C:L.45, C:N.49, C:E.100, C:E.100, C:G.102, A:T.29, A:R.34, A:V.35, A:G.55, A:G.55 Water bridges: C:G.42, C:G.42, C:G.102, C:A.104, C:A.104, C:T.105, A:V.35, A:Q.116 pi-Stacking: C:F.44, C:F.44 pi-Cation interactions: A:R.34, A:R.34 2BA.3: 21 residues within 4Å: Chain A: V.15, G.42, G.43, F.44, L.45, N.49, V.99, E.100, V.101, G.102, T.105, F.107 Chain B: T.29, N.32, F.33, R.34, V.35, T.36, M.53, I.54, G.55 25 PLIP interactions: 16 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:G.42, A:G.43, A:F.44, A:L.45, A:N.49, A:E.100, A:E.100, A:G.102, B:T.29, B:R.34, B:V.35, B:G.55, B:G.55 Water bridges: A:G.42, A:G.42, A:G.102, A:A.104, A:A.104, A:T.105, B:V.35, B:Q.116 pi-Stacking: A:F.44, A:F.44 pi-Cation interactions: B:R.34, B:R.34 2BA.5: 21 residues within 4Å: Chain B: V.15, G.42, G.43, F.44, L.45, N.49, V.99, E.100, V.101, G.102, T.105, F.107 Chain C: T.29, N.32, F.33, R.34, V.35, T.36, M.53, I.54, G.55 25 PLIP interactions: 16 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:G.42, B:G.43, B:F.44, B:L.45, B:N.49, B:E.100, B:E.100, B:G.102, C:T.29, C:R.34, C:V.35, C:G.55, C:G.55 Water bridges: B:G.42, B:G.42, B:G.102, B:A.104, B:A.104, B:T.105, C:V.35, C:Q.116 pi-Stacking: B:F.44, B:F.44 pi-Cation interactions: C:R.34, C:R.34

3 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.4, NI.6 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:H.4, C:H.6, B:H.4, B:H.6, A:H.4, A:H.6 NI.4: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.2, NI.6 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:H.4, C:H.6, B:H.4, B:H.6, A:H.4, A:H.6 NI.6: 8 residues within 4Å: Chain A: H.4, H.6 Chain B: H.4, H.6 Chain C: H.4, H.6 Ligands: NI.2, NI.4 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:H.4, C:H.6, B:H.4, B:H.6, A:H.4, A:H.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gundlach, J. et al., Identification, Characterization, and Structure Analysis of the Cyclic di-AMP-binding PII-like Signal Transduction Protein DarA. J.Biol.Chem. (2015)

Release Date

2014-12-03

Peptides

Uncharacterized protein YaaQ: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Uncharacterized protein YaaQ