SMTL ID : 4mdz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

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

5 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 10 residues within 4Å: Chain A: D.228, K.231, W.250, M.253, H.256, H.283, Y.291 Ligands: FE.1, FE.2, SIN.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.291 Water bridges: A:H.283 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.283, 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 Water bridges: A:E.191, A:D.311 SIN.6: 8 residues within 4Å: Chain A: S.182, H.183, T.185, K.186, D.189, E.191, I.196, D.228 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.191, A:I.196 Hydrogen bonds: A:T.185, A:D.189, A:E.191, A:E.191 Water bridges: A:E.191, A:H.195, A:D.228 Salt bridges: A:H.183 SIN.7: 12 residues within 4Å: Chain A: E.281, E.284, R.285, W.286, I.300, G.304, R.305, S.308, I.309, H.342, F.343, D.344 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.286, A:I.300, A:R.305 Hydrogen bonds: A:E.284, A:S.308, A:D.344 SIN.8: 11 residues within 4Å: Chain A: K.188, K.231, V.232, I.234, D.236, L.239 Chain B: T.185, K.188, K.231, V.232, L.239 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.232, B:K.188 Hydrogen bonds: A:V.232 Water bridges: A:K.188, A:D.236, B:K.188, B:K.188 Salt bridges: A:K.188, A:K.188, B:K.188, B:K.188

1 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)

C2E.10: 15 residues within 4Å: Chain B: K.231, K.241, G.243, L.245, W.250, H.283, Y.291, D.311, V.312, A.315, L.316, R.320, K.323, F.334, H.342 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.231, B:K.241, B:G.243, B:R.320 Water bridges: B:R.285, B:Y.291 Salt bridges: B:H.283

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

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