SMTL ID : 8iju.1

ATP-dependent RNA helicase DDX39A (URH49delta41)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

PGE.1: 10 residues within 4Å: Chain A: S.59, G.60, N.313, L.314, F.315, G.316, R.317, H.341, R.345 Ligands: EDO.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.314, A:G.316, A:G.316, A:H.341, A:R.345 Water bridges: A:S.59, A:R.345

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: K.58, S.59, G.60, K.63, T.64, G.316, R.317, G.318 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.60, A:K.63, A:T.64, A:T.64, A:G.316, A:G.318 Water bridges: A:M.61, A:M.61, A:M.61, A:G.62, A:K.63, A:K.63, A:T.64, A:A.65 Salt bridges: A:K.63 PO4.3: 6 residues within 4Å: Chain A: R.103, M.289, A.290, Q.291, R.294, R.317 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.291 Water bridges: A:R.103, A:R.317, A:R.317 Salt bridges: A:R.103, A:R.294, A:R.317

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

EDO.4: 5 residues within 4Å: Chain A: F.33, L.295, Y.298, M.319, D.320 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: G.50, K.190, Q.191 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: A.197, D.337, T.338, H.341 Ligands: PGE.1 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: G.80, Q.81, V.82, L.129, C.133, P.134, F.153 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: V.115, F.116, F.117, G.118, G.119, L.120, D.125, R.143 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: F.33, Q.40, G.62, A.65, G.318, D.320 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: K.201, R.204, R.208, F.218 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: H.41, E.42, P.45 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: E.102, S.105, K.106, M.108, P.109, V.111 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.200, K.201, K.224, R.374 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: L.230, Q.231, Q.232, N.378, A.380 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: S.13, R.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.58, M.61, R.323, A.344, R.345 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: Q.266 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: N.363, D.364, I.367 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: Y.233, I.388 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: G.118, G.119, L.120, S.121 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: P.77, V.78, N.79 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujita, K.I. et al., Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nat Commun (2024)

Release Date

2024-01-24

Peptides

ATP-dependent RNA helicase DDX39A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase DDX39A