SMTL ID : 3fkq.1

Crystal structure of NtrC-like two-domain protein (RER070207001320) from Eubacterium rectale at 2.10 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: G.153, G.154, V.155, G.156, T.157, S.158, T.159, E.181, N.326, K.327, P.348, R.349, Y.350, I.358 Chain B: G.153, S.292, L.294, K.298 Ligands: MG.2, GOL.14 25 PLIP interactions: 17 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.154, A:V.155, A:G.156, A:T.157, A:T.157, A:S.158, A:T.159, A:T.159, A:N.326, A:K.327, A:K.327, A:P.348, A:Y.350, B:G.153, B:S.292, B:S.292 Water bridges: A:T.157, A:S.158, A:S.158, A:S.158, B:P.151, B:K.298 Salt bridges: B:K.298, B:K.298, B:K.298 ATP.9: 20 residues within 4Å: Chain A: G.153, S.292, L.294, K.298 Chain B: G.153, G.154, V.155, G.156, T.157, S.158, T.159, E.181, N.326, K.327, P.348, R.349, Y.350, I.358 Ligands: GOL.6, MG.10 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.154, B:V.155, B:G.156, B:T.157, B:T.157, B:T.157, B:S.158, B:T.159, B:T.159, B:N.326, B:K.327, B:K.327, B:P.348, B:Y.350, A:G.153, A:S.292, A:S.292 Water bridges: B:S.158, B:S.158, B:S.158, A:P.151, A:K.298 Salt bridges: A:K.298, A:K.298, A:K.298

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.158, E.181 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.158, A:E.181, H2O.1, H2O.2 MG.10: 3 residues within 4Å: Chain B: S.158, E.181 Ligands: ATP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.158, B:E.181, H2O.6, H2O.7

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: S.329, N.330, K.331 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: S.329, N.330, K.331 Ligand excluded by PLIP

4 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.4: 4 residues within 4Å: Chain A: M.171, G.172, K.173, D.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.173 2PE.5: 4 residues within 4Å: Chain A: M.300, Y.303, E.304, V.307 No protein-ligand interaction detected (PLIP) 2PE.12: 4 residues within 4Å: Chain B: M.171, G.172, K.173, D.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.173 2PE.13: 4 residues within 4Å: Chain B: M.300, Y.303, E.304, V.307 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.304

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: S.292, Q.293, L.294, N.332 Chain B: A.353, V.355, I.358 Ligands: ATP.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.292, A:Q.293, A:L.294, A:N.332, A:N.332 GOL.7: 5 residues within 4Å: Chain A: R.349, E.351, H.352 Chain B: S.329, N.332 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.349, A:R.349, A:E.351, A:E.351, B:S.329, B:N.332 Water bridges: A:A.353, A:A.353 GOL.14: 8 residues within 4Å: Chain A: A.353, V.355, I.358 Chain B: S.292, Q.293, L.294, N.332 Ligands: ATP.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.292, B:Q.293, B:L.294, B:N.332, B:N.332 GOL.15: 5 residues within 4Å: Chain A: S.329, N.332 Chain B: R.349, E.351, H.352 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.329, A:N.332, B:R.349, B:R.349, B:E.351 Water bridges: B:A.353, B:A.353

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain A: E.272, I.273 Chain B: L.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.273 SO4.16: 3 residues within 4Å: Chain A: L.240 Chain B: E.272, I.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization. Mol.Microbiol. (2012)

Release Date

2009-01-06

Peptides

NtrC-like two-domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NtrC-like two-domain protein