SMTL ID : 4mcw.1

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

6 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.228, H.256, H.282, H.283 Ligands: FE.2, SIN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.228, A:H.256, A:H.282, A:H.283, H2O.3 FE.2: 7 residues within 4Å: Chain A: E.191, D.228, K.231 Ligands: FE.1, FE.3, SIN.4, SIN.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.191, A:D.228, H2O.3, H2O.3 FE.3: 7 residues within 4Å: Chain A: E.191, H.195, H.227, D.311 Ligands: FE.2, SIN.5, IMD.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.191, A:H.195, A:D.311, H2O.3 FE.9: 6 residues within 4Å: Chain B: D.228, H.256, H.282, H.283 Ligands: FE.10, SIN.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.228, B:H.256, B:H.282, B:H.283, H2O.14 FE.10: 7 residues within 4Å: Chain B: E.191, D.228, K.231 Ligands: FE.9, FE.11, SIN.12, SIN.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.191, B:D.228, H2O.11, H2O.14 FE.11: 7 residues within 4Å: Chain B: E.191, H.195, H.227, D.228, D.311 Ligands: FE.10, SIN.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.191, B:H.195, B:D.311, H2O.11, H2O.11

6 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 11 residues within 4Å: Chain A: E.191, D.228, K.231, W.250, M.253, H.256, H.283, Y.291 Ligands: FE.1, FE.2, SIN.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.291 Salt bridges: A:K.231, A:H.256, A:H.256, A:H.283, A:H.283 SIN.5: 8 residues within 4Å: Chain A: E.191, H.195, D.311, V.312, A.315 Ligands: FE.2, FE.3, SIN.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.315 Salt bridges: A:H.195, A:K.231 SIN.6: 12 residues within 4Å: Chain A: S.182, T.185, D.189, E.191, I.196, P.225, M.226, H.227, D.228, I.229, K.231 Ligands: IMD.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.196, A:D.228 Hydrogen bonds: A:S.182, A:E.191, A:D.228 Salt bridges: A:H.227, A:K.231 SIN.12: 11 residues within 4Å: Chain B: E.191, D.228, K.231, W.250, M.253, H.256, H.283, Y.291 Ligands: FE.9, FE.10, SIN.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.291 Salt bridges: B:K.231, B:H.256, B:H.256, B:H.283, B:H.283 SIN.13: 9 residues within 4Å: Chain B: E.191, H.195, H.283, D.311, V.312, A.315 Ligands: FE.10, FE.11, SIN.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.315 Salt bridges: B:K.231 SIN.14: 5 residues within 4Å: Chain B: W.326, R.330, R.333, F.334, E.337 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.333, B:F.334 Hydrogen bonds: B:F.334 Water bridges: B:R.333 Salt bridges: B:R.330

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 11 residues within 4Å: Chain A: E.191, H.195, I.196, V.199, A.224, P.225, H.227, D.228, D.311 Ligands: FE.3, SIN.6 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.227

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

EDO.8: 4 residues within 4Å: Chain A: Y.95, R.102, D.105, K.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.95, A:Y.95, A:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellini, D. et al., Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol.Microbiol. (2014)

Release Date

2014-02-19

Peptides

Metal dependent phosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metal dependent phosphohydrolase

Related Entries With Identical Sequence