SMTL ID : 1k20.1

Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.8, D.12, D.76 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.8, A:D.12, A:D.12, A:D.76, H2O.1 MN.2: 7 residues within 4Å: Chain A: D.14, D.76, H.98, H.99, A.120, D.150 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:D.76, A:H.98, A:D.150, H2O.1 MN.6: 5 residues within 4Å: Chain B: H.8, D.12, A.15, D.76 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.8, B:D.12, B:D.76, H2O.14, H2O.14 MN.7: 6 residues within 4Å: Chain B: D.14, D.76, H.98, H.99, D.150 Ligands: MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.14, B:D.76, B:H.98, B:D.150, H2O.14

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

SO4.3: 4 residues within 4Å: Chain A: H.99, K.206, R.296, K.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.296, A:K.297 Water bridges: A:R.296 Salt bridges: A:H.99, A:K.206, A:R.296 SO4.4: 5 residues within 4Å: Chain A: E.91, V.92, T.106, A.107, N.108 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.92, A:A.107, A:N.108, A:N.108 Water bridges: A:E.91, A:E.91, A:E.105 SO4.8: 4 residues within 4Å: Chain B: H.99, K.206, R.296, K.297 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.296, B:K.297 Water bridges: B:K.206, B:K.206 Salt bridges: B:H.99, B:K.206, B:R.296 SO4.9: 5 residues within 4Å: Chain B: E.91, V.92, T.106, A.107, N.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.92, B:A.107, B:N.108, B:N.108 Water bridges: B:E.91, B:E.91

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.45, G.189, D.204, Q.219, V.220, N.221 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.189, A:D.204, A:D.204, A:N.221 Water bridges: A:N.43, A:E.44, A:N.221 GOL.10: 6 residues within 4Å: Chain B: E.45, G.189, D.204, Q.219, V.220, N.221 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.189, B:D.204, B:N.221 Water bridges: B:E.45, B:G.189, B:N.221 GOL.11: 5 residues within 4Å: Chain B: V.223, D.224, I.225, A.226, D.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.225, B:A.226, B:D.257 Water bridges: B:N.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, S. et al., The "open" and "closed" structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii. J.Mol.Biol. (2001)

Release Date

2001-10-31

Peptides

Manganese-dependent inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Manganese-dependent inorganic pyrophosphatase