SMTL ID : 5u7x.1

Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.41, K.65, Y.325, E.412 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.325, A:E.412 Water bridges: A:K.65, A:K.65 Salt bridges: A:R.41, A:K.65 PO4.2: 10 residues within 4Å: Chain A: G.36, S.37, T.110, A.111, E.153, G.182, G.183, A.184, S.185 Ligands: MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.37, A:S.37, A:T.110, A:T.110, A:A.111, A:G.183, A:A.184, A:S.185, A:S.185 Water bridges: A:E.153, A:E.153, A:E.153

1 x MN: MANGANESE (II) ION(Non-functional Binders)

MN.3: 1 residues within 4Å: Ligands: PO4.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Summers, E.L. et al., Structures and kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion catalytic mechanism. Protein Sci. (2017)

Release Date

2017-05-31

Peptides

Nod factor binding lectin-nucleotide phosphohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

Nod factor binding lectin-nucleotide phosphohydrolase