SMTL ID : 5a61.1

Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two manganese ions.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.1: 14 residues within 4Å: Chain A: E.6, E.8, K.10, R.58, R.60, K.71, R.83, F.126, R.128, E.162, S.192, K.193 Ligands: MN.2, MN.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.193 Water bridges: A:Y.42, A:R.60, A:K.71, A:A.194, A:A.194 Salt bridges: A:K.10, A:K.10, A:R.58, A:R.58, A:R.60, A:R.60, A:K.71, A:K.71, A:K.71, A:R.83, A:R.128, A:R.128, A:K.193, A:K.193

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: E.8, E.162 Ligands: 3PO.1, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:E.162, A:E.162 MN.3: 6 residues within 4Å: Chain A: E.6, E.8, E.162, E.164 Ligands: 3PO.1, MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.6, A:E.8, A:E.164, H2O.1, H2O.1

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

EDO.4: 5 residues within 4Å: Chain A: E.254, R.404, H.405, A.408, T.409 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.404, A:R.404, A:H.405 Water bridges: A:E.254 EDO.5: 4 residues within 4Å: Chain A: R.350, H.351, R.373, R.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.350, A:R.373, A:R.373 EDO.6: 6 residues within 4Å: Chain A: R.22, P.35, Y.127, E.129, L.144, Q.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.22, A:E.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez, J. et al., Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J.Biol.Chem. (2015)

Release Date

2015-08-05

Peptides

INORGANIC TRIPHOSPHATASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

INORGANIC TRIPHOSPHATASE

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