SMTL ID : 5tef.1

Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x GTG: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE(Non-covalent)

GTG.1: 15 residues within 4Å: Chain A: Y.402, Y.493, T.494, T.559, E.560, L.599, V.600, N.601, K.660, T.662, Y.679, R.703, L.705 Ligands: UNX.8, UNX.21 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.493, A:T.559, A:T.559, A:K.660, A:Y.679, A:Y.679, A:R.703 Salt bridges: A:E.560, A:K.660, A:K.660 pi-Stacking: A:Y.493, A:Y.493

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.30, P.31, N.32, W.33, R.378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.33, A:R.378, A:R.378 Water bridges: A:S.30, A:W.33 GOL.3: 5 residues within 4Å: Chain A: Y.34, S.132, I.173, F.174, W.305 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.132, A:E.149 Water bridges: A:R.85, A:R.85, A:R.85 GOL.4: 7 residues within 4Å: Chain A: H.309, P.311, S.312, N.313, P.361, Q.363, Q.369 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.312, A:N.313, A:N.313, A:Q.369 Water bridges: A:L.362, A:Q.363, A:Q.363

19 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 3 residues within 4Å: Chain A: S.562, W.563, W.605 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: T.307, L.308, N.358, L.359 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: Q.317, Q.329 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: N.601, T.662 Ligands: GTG.1 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: T.341, L.342, A.345, L.388 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: S.407, V.409, W.453, G.459 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: T.53, S.54 Ligands: UNX.12 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain A: T.53, V.80, G.81, H.82 Ligands: UNX.11 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: R.698, H.700, Q.701 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: W.392, T.393, N.433 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain A: S.403, A.450, L.451 Ligands: UNX.16 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain A: L.451, T.494, L.495 Ligands: UNX.15, UNX.17 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain A: C.452, L.495 Ligands: UNX.16 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: C.460, Y.473, D.474 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: A.665, V.707, A.708 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: S.403, L.404, C.706 Ligand excluded by PLIP UNX.21: 5 residues within 4Å: Chain A: L.599, N.601, N.624, K.660 Ligands: GTG.1 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: E.228, Y.260 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain A: Q.369, D.384, I.385, A.386 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes Dev. (2016)

Release Date

2016-10-19

Peptides

Gem-associated protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Gem-associated protein 5

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