SMTL ID : 5tee.1

Crystal structure of Gemin5 WD40 repeats in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.30, P.31, N.32, W.33, R.378, G.398 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.33, A:R.378, A:R.378 Water bridges: A:S.30, A:W.33, A:R.52 GOL.2: 6 residues within 4Å: Chain A: Y.34, S.132, I.173, F.174, W.305 Ligands: UNX.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.132 Water bridges: A:R.85, A:R.85, A:R.85 GOL.3: 3 residues within 4Å: Chain A: D.687, R.690, L.694 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.673, A:D.687

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

UNX.4: 3 residues within 4Å: Chain A: G.96, Q.97, Y.98 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: P.43, L.362, Q.363 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: T.682, R.698, P.740 Ligands: NA.40 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: F.697, Q.734 Ligands: UNX.8 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: P.24, F.697 Ligands: UNX.7 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain A: R.354 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: E.149, K.150, T.172 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: W.532 Ligand excluded by PLIP UNX.12: 4 residues within 4Å: Chain A: A.405, L.451, C.452 Ligands: UNX.13 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: S.403, L.404, L.451 Ligands: UNX.12, UNX.25 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: L.308, H.309, L.359 Ligands: UNX.15 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: H.309, P.361 Ligands: UNX.14 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: G.108, H.127 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: R.37, T.177, I.220 Ligands: UNX.21 Ligand excluded by PLIP UNX.18: 5 residues within 4Å: Chain A: T.494, E.560, N.601, T.602 Ligands: UNX.19 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: Y.493, T.494 Ligands: UNX.18 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: T.130, I.131, S.132, E.149 Ligands: GOL.2 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain A: R.37, H.135, T.177 Ligands: UNX.17 Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain A: V.557, E.575 Ligands: UNX.23 Ligand excluded by PLIP UNX.23: 5 residues within 4Å: Chain A: P.556, V.557, E.575, D.576 Ligands: UNX.22 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain A: S.562, W.563, S.604, W.605 Ligand excluded by PLIP UNX.25: 4 residues within 4Å: Chain A: S.403, A.450, L.451 Ligands: UNX.13 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: Q.482, I.483 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain A: I.194, V.195, L.210, R.211 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: E.575, K.598, L.599 Ligand excluded by PLIP UNX.29: 2 residues within 4Å: Chain A: F.154, S.163 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: H.309, P.311 Ligands: UNX.32 Ligand excluded by PLIP UNX.31: 4 residues within 4Å: Chain A: D.671, G.672, R.673, D.687 Ligand excluded by PLIP UNX.32: 5 residues within 4Å: Chain A: P.311, S.312, N.313, Q.369 Ligands: UNX.30 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain A: V.437 Ligands: UNX.34 Ligand excluded by PLIP UNX.34: 5 residues within 4Å: Chain A: D.379, P.395, V.437 Ligands: UNX.33, UNX.35 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain A: P.395, V.437, N.439 Ligands: UNX.34 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain A: N.439, F.440 Ligand excluded by PLIP UNX.37: 1 residues within 4Å: Chain A: R.698 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain A: R.171, D.192 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.39: 2 residues within 4Å: Chain A: A.125, H.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.127 NA.40: 3 residues within 4Å: Chain A: R.698, H.700 Ligands: UNX.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.698

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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