SMTL ID : 4urs.1

Crystal Structure of GGDEF domain from T.maritima

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: G.57, P.157 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain B: L.94, R.99 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain B: H.30, D.31, P.32, N.38 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.30, B:D.31, B:N.38

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 4 residues within 4Å: Chain A: K.58, D.117 Chain B: E.56 Ligands: C2E.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.117 Salt bridges: A:K.58 Hydrogen bonds: B:E.56

4 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.3: 8 residues within 4Å: Chain A: D.95, R.96, V.97, R.98, R.99, R.129 Chain B: R.55 Ligands: C2E.4 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.96, A:R.98, A:R.99, A:R.129, B:R.55, B:R.55, B:R.55 pi-Cation interactions: A:R.129, B:R.55 Water bridges: B:R.55, B:R.55 C2E.4: 14 residues within 4Å: Chain A: V.97, R.98, D.101, L.115, Y.116, D.117, M.118, K.119, Y.122, L.126, R.129 Chain B: R.55 Ligands: MES.2, C2E.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.98, A:Y.116, A:K.119, A:R.129, A:R.129, B:R.55, B:R.55 Salt bridges: A:R.98, A:D.101, A:K.119 pi-Cation interactions: A:R.98 C2E.5: 12 residues within 4Å: Chain A: R.55 Chain B: R.98, D.101, L.115, Y.116, D.117, M.118, K.119, Y.122, L.126, R.129 Ligands: C2E.8 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.98, B:R.98, B:Y.116, B:R.129, B:R.129, A:R.55, A:R.55 Water bridges: B:K.119 Salt bridges: B:R.98, B:D.101, B:K.119 pi-Cation interactions: B:R.98 C2E.8: 9 residues within 4Å: Chain A: R.55 Chain B: D.95, R.96, V.97, R.98, R.99, Y.122, R.129 Ligands: C2E.5 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.98, B:R.99, B:Y.122, B:R.129, A:R.55, A:R.55, A:R.55 Salt bridges: B:R.99, A:R.55 pi-Cation interactions: B:R.129, A:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deepthi, A. et al., Structure of a Diguanylate Cyclase from Thermotoga Maritima: Insights Into Activation, Feedback Inhibition and Thermostability. Plos One (2014)

Release Date

2014-10-08

Peptides

DIGUANYLATE CYCLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIGUANYLATE CYCLASE