SMTL ID : 7v4e.1

Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: G.194, T.195, G.196, K.197, E.198, N.257 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.192, A:G.194, A:T.195, A:T.195, A:G.196, A:K.197, A:E.198, A:N.257 Salt bridges: A:K.197 SO4.2: 5 residues within 4Å: Chain B: S.193, G.194, G.196, K.197, E.198 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.196, B:K.197, B:E.198 Salt bridges: B:K.197

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)(Non-functional Binders)

C2E.3: 4 residues within 4Å: Chain B: R.374, E.375, Q.379 Ligands: C2E.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.374, B:E.375, B:Q.379 C2E.4: 1 residues within 4Å: Ligands: C2E.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakrabortty, T. et al., Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding. J.Mol.Biol. (2022)

Release Date

2022-04-06

Peptides

VpsR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

VpsR

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