SMTL ID : 6qva.1

Crystal structure of a CHAD domain from Chlorobium tepidum in complex with inorganic polyphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: G.80, E.83, Y.137, E.142, Y.143, F.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137, A:Y.137 EDO.2: 9 residues within 4Å: Chain A: I.39, D.42, D.44, S.45, F.47, L.48, L.91, D.95, K.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.47, A:L.48, A:D.95 EDO.3: 3 residues within 4Å: Chain A: D.70, E.72, K.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.72 EDO.4: 5 residues within 4Å: Chain A: H.18, E.156, E.158, L.159, P.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.18, A:E.156 EDO.8: 6 residues within 4Å: Chain B: G.80, E.83, Y.137, E.142, Y.143, F.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.137 EDO.9: 9 residues within 4Å: Chain B: I.39, D.42, D.44, S.45, F.47, L.48, L.91, D.95, K.127 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.42, B:F.47, B:L.48, B:D.95 EDO.10: 3 residues within 4Å: Chain B: D.70, E.72, K.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.70, B:E.72 EDO.11: 5 residues within 4Å: Chain B: H.18, E.156, E.158, L.159, P.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.18, B:E.156

2 x 9PI: bis[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate(Non-covalent)

9PI.5: 9 residues within 4Å: Chain A: H.49, R.52, V.53, R.56, R.92, R.207, K.211, R.214, E.218 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.92, A:R.207 Water bridges: A:R.52, A:R.52, A:R.52, A:R.56, A:R.56, A:R.207, A:K.211 Salt bridges: A:H.49, A:H.49, A:R.52, A:R.52, A:R.56, A:R.56, A:R.56, A:R.56, A:R.92, A:R.207, A:K.211, A:K.211, A:K.211, A:R.214, A:K.237 9PI.12: 9 residues within 4Å: Chain B: H.49, R.52, V.53, R.56, R.92, R.207, K.211, R.214, E.218 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:R.92, B:R.207 Water bridges: B:R.52, B:R.52, B:R.52, B:R.56, B:R.56, B:R.207, B:K.211 Salt bridges: B:H.49, B:H.49, B:R.52, B:R.52, B:R.56, B:R.56, B:R.56, B:R.56, B:R.92, B:R.207, B:K.211, B:K.211, B:K.211, B:R.214, B:K.237

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.6: 3 residues within 4Å: Chain A: K.182, K.186, H.190 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:K.182, A:K.186, A:K.186, A:K.186, A:H.190 3PO.13: 3 residues within 4Å: Chain B: K.182, K.186, H.190 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:K.182, B:K.186, B:K.186, B:K.186, B:H.190

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

PO4.7: 6 residues within 4Å: Chain A: S.16, H.18, E.19, R.22, G.157, L.159 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.16, A:E.19, A:E.19, A:G.157 Water bridges: A:S.16, A:S.16 Salt bridges: A:H.18, A:R.22 PO4.14: 6 residues within 4Å: Chain B: S.16, H.18, E.19, R.22, G.157, L.159 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:E.19, B:G.157 Water bridges: B:S.16, B:S.16 Salt bridges: B:H.18, B:R.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorenzo-Orts, L. et al., Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules. Life Sci Alliance (2019)

Release Date

2019-05-29

Peptides

CHAD domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CHAD domain

Related Entries With Identical Sequence