SMTL ID : 4yix.1

Structure of MRB1590 bound to ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.319, S.320, D.409, D.411, V.456 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: C.570, C.620, Q.624 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.570, A:C.620 MG.3: 4 residues within 4Å: Chain A: C.570, L.574, C.620, I.651 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.620 MG.16: 6 residues within 4Å: Chain B: K.319, S.320, D.409, D.411, V.456 Ligands: ADP.30 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain B: C.570, C.620, Q.624 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.570, B:C.620 MG.18: 4 residues within 4Å: Chain B: C.570, L.574, C.620, I.651 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.620

22 x HG: MERCURY (II) ION(Non-covalent)

HG.4: 3 residues within 4Å: Chain A: Y.252, F.255, C.288 Ligand excluded by PLIP HG.5: 3 residues within 4Å: Chain A: C.107, F.109, L.111 Ligand excluded by PLIP HG.6: 5 residues within 4Å: Chain A: N.124, C.126, H.238, E.241, V.601 Ligand excluded by PLIP HG.7: 5 residues within 4Å: Chain A: L.408, D.409, E.410, C.413, M.418 Ligand excluded by PLIP HG.8: 3 residues within 4Å: Chain A: D.480, C.481, E.484 Ligand excluded by PLIP HG.9: 3 residues within 4Å: Chain A: C.514, F.515, V.664 Ligand excluded by PLIP HG.10: 2 residues within 4Å: Chain A: C.621, T.646 Ligand excluded by PLIP HG.11: 4 residues within 4Å: Chain A: Q.569, L.631, C.636, L.638 Ligand excluded by PLIP HG.12: 3 residues within 4Å: Chain A: S.138, G.142, C.221 Ligand excluded by PLIP HG.13: 5 residues within 4Å: Chain A: C.105, I.186, I.188, L.218, V.222 Ligand excluded by PLIP HG.14: 2 residues within 4Å: Chain A: C.236, Y.341 Ligand excluded by PLIP HG.19: 3 residues within 4Å: Chain B: Y.252, F.255, C.288 Ligand excluded by PLIP HG.20: 3 residues within 4Å: Chain B: C.107, F.109, L.111 Ligand excluded by PLIP HG.21: 5 residues within 4Å: Chain B: N.124, C.126, H.238, E.241, V.601 Ligand excluded by PLIP HG.22: 5 residues within 4Å: Chain B: L.408, D.409, E.410, C.413, M.418 Ligand excluded by PLIP HG.23: 3 residues within 4Å: Chain B: D.480, C.481, E.484 Ligand excluded by PLIP HG.24: 3 residues within 4Å: Chain B: C.514, F.515, V.664 Ligand excluded by PLIP HG.25: 2 residues within 4Å: Chain B: C.621, T.646 Ligand excluded by PLIP HG.26: 4 residues within 4Å: Chain B: Q.569, L.631, C.636, L.638 Ligand excluded by PLIP HG.27: 3 residues within 4Å: Chain B: S.138, G.142, C.221 Ligand excluded by PLIP HG.28: 5 residues within 4Å: Chain B: C.105, I.186, I.188, L.218, V.222 Ligand excluded by PLIP HG.29: 2 residues within 4Å: Chain B: C.236, Y.341 Ligand excluded by PLIP

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.15: 17 residues within 4Å: Chain A: P.263, L.273, N.276, A.277, V.278, G.314, G.315, F.316, H.317, G.318, K.319, S.320, T.321, Y.476 Chain B: D.384, S.386 Ligands: MG.1 22 PLIP interactions: 17 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.278, A:V.278, A:F.316, A:H.317, A:G.318, A:K.319, A:S.320, A:S.320, A:T.321, A:T.321, B:D.384, B:D.384, B:S.386 Water bridges: A:K.319, A:S.320, A:R.324, A:R.324, B:R.356, B:G.387 Salt bridges: A:K.319 pi-Stacking: A:Y.476, A:Y.476 ADP.30: 17 residues within 4Å: Chain A: D.384, S.386 Chain B: P.263, L.273, N.276, A.277, V.278, G.314, G.315, F.316, H.317, G.318, K.319, S.320, T.321, Y.476 Ligands: MG.16 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:V.278, B:V.278, B:F.316, B:H.317, B:G.318, B:K.319, B:S.320, B:S.320, B:T.321, B:T.321, B:Y.476, A:D.384, A:D.384, A:S.386 Water bridges: B:K.319, B:S.320, B:R.324, A:D.355, A:R.356, A:G.387 Salt bridges: B:K.319 pi-Stacking: B:Y.476, B:Y.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaw, P.L. et al., Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. Nucleic Acids Res. (2015)

Release Date

2015-08-12

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uncharacterized protein