SMTL ID : 6d9m.1

T4-Lysozyme fusion to Geobacter GGDEF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 10 residues within 4Å: Chain A: K.16, S.231, V.232, R.233, D.236, V.251, E.252, T.253, V.261, R.264 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.16, A:K.16, A:R.233, A:V.251, A:V.251, A:T.253, A:R.264, A:R.264 Salt bridges: A:D.236 pi-Cation interactions: A:R.233 GTP.2: 10 residues within 4Å: Chain A: T.21, N.144, R.148, I.179, D.182, R.183, K.186, R.187, R.190 Ligands: ACT.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.21, A:N.144, A:R.148, A:R.148, A:R.183, A:K.186, A:K.186 Water bridges: A:Y.18, A:Y.18, A:T.21, A:N.144, A:R.187, A:R.187, A:R.187 Salt bridges: A:D.182, A:R.187, A:R.190

1 x GMP: GUANOSINE(Non-covalent)

GMP.3: 12 residues within 4Å: Chain A: L.168, F.205, K.206, N.209, H.214, G.217, S.218, L.221, R.240, G.243, D.244 Ligands: POP.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.209, A:N.209, A:S.218, A:R.240 Water bridges: A:R.240, A:G.243, A:D.244

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 11 residues within 4Å: Chain A: D.201, L.202, D.203, F.204, F.205, K.206, D.244, K.315, K.319 Ligands: GMP.3, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.201, A:F.204, A:F.205, A:K.206 Water bridges: A:K.206, A:K.206 Salt bridges: A:K.206, A:K.315, A:K.319

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.201, L.202, D.244, K.315 Ligands: POP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, A:L.202, A:D.244, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: A.259, E.263, Y.290, V.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.263, A:V.322 Water bridges: A:R.324

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: T.142, P.143, N.144, R.145 Ligands: GTP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.144, A:N.144, A:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hallberg, Z.F. et al., Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration. Elife (2019)

Release Date

2019-04-10

Peptides

Fusion protein of Endolysin,Response receiver sensor diguanylate cyclase, GAF domain-containing: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fusion protein of Endolysin,Response receiver sensor diguanylate cyclase, GAF domain-containing