SMTL ID : 4h54.1

Crystal structure of the diguanylate cyclase DgcZ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.22, H.79, H.83 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.22, A:H.79, A:H.83 ZN.6: 3 residues within 4Å: Chain B: H.22, H.79, H.83 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.22, B:H.79, B:H.83

4 x GAV: GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE(Non-covalent)

GAV.2: 20 residues within 4Å: Chain A: L.134, D.165, I.166, D.167, R.168, F.169, K.170, N.173, H.178, G.181, D.182, L.185, R.204, G.207, E.208, K.277, R.281 Chain B: R.140, Y.205 Ligands: MG.3 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:R.140, B:R.140, B:Y.205, A:R.168, A:F.169, A:K.170, A:K.170, A:N.173, A:N.173, A:H.178, A:R.204, A:R.204 pi-Cation interactions: B:R.140, B:R.140 Salt bridges: A:D.182, A:K.277, A:R.281 GAV.4: 9 residues within 4Å: Chain A: Y.199, E.200, V.214, K.215, A.216, R.224, A.225, R.228 Ligands: C2E.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.199, A:K.215, A:R.228 Salt bridges: A:E.200 pi-Cation interactions: A:R.197 GAV.7: 19 residues within 4Å: Chain A: R.140, E.209 Chain B: L.134, D.165, I.166, D.167, R.168, F.169, K.170, N.173, H.178, D.182, L.185, R.204, G.207, E.208, K.277, R.281 Ligands: MG.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.168, B:F.169, B:K.170, B:N.173, B:N.173, B:H.178, B:R.204, B:R.204, A:R.140 Salt bridges: B:D.182, B:K.277, B:R.281 GAV.9: 7 residues within 4Å: Chain B: R.197, Y.199, E.200, K.215, R.224, A.225, R.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.199, B:R.228 Salt bridges: B:E.200 pi-Cation interactions: B:R.197

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.165, I.166, E.208, K.277 Ligands: GAV.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:I.166, A:E.208, A:E.208 MG.8: 7 residues within 4Å: Chain B: D.165, I.166, D.167, R.168, E.208, K.277 Ligands: GAV.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.165, B:I.166, B:E.208, B:E.208

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.5: 7 residues within 4Å: Chain A: S.194, W.195, T.196, R.197, D.198, R.228 Ligands: GAV.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.197, A:D.198 pi-Cation interactions: A:R.228, A:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahringer, F. et al., Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. Structure (2013)

Release Date

2013-07-03

Peptides

Diguanylate cyclase YdeH: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diguanylate cyclase YdeH