SMTL ID : 3hax.1

Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 4 residues within 4Å: Chain A: E.41, W.227, K.228, G.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 PGE.2: 6 residues within 4Å: Chain A: V.18, I.20, W.254, K.276, L.292, D.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.276, A:L.292

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: E.131, F.132 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain C: G.106, K.107, R.109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.107

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.8, C.11, C.20, C.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.8, B:C.11, B:C.20, B:C.23

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain A: P.55 Chain B: P.32, P.33, R.34 Chain C: E.62, I.63, H.66 Chain D: U.32 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.55, B:R.34, B:R.34

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain D: C.37 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Mol.Cell (2009)

Release Date

2009-06-23

Peptides

Probable tRNA pseudouridine synthase B: A
Ribosome biogenesis protein Nop10: B
50S ribosomal protein L7Ae: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Probable tRNA pseudouridine synthase B

Ribosome biogenesis protein Nop10

50S ribosomal protein L7Ae

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