MolNFT v1 · #134117 · protein + RNA

Crystal structure of the SUB2-YRA1 complex in association with RNA

5SUP · ATP-dependent RNA helicase SUB2: “Crystal structure of the SUB2-YRA1 complex in association with RNA”. X-ray diffraction, 3 ligands (ADP, BEF, MG), 15 pockets (best druggability 0.85). MolNFT v1 #134117 on GenesisL1: 3D structure…

PDB: 5SUP
Type: protein + RNA
Length: 1,214 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent RNA helicase SUB2; RNA annealing protein YRA1; RNA…
EC: 3.6.4.13
UniProt: Q07478, Q12159
Ligands: ADP, BEF, MG
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ATP-dependent RNA helicase SUB2 (EC 3.6.4.13)	protein	383	42% helix, 17% strand	Q07478
C	ATP-dependent RNA helicase SUB2 (EC 3.6.4.13)	protein	381	41% helix, 17% strand	Q07478
G, H	RNA annealing protein YRA1	protein	17	65% helix, 0% strand	Q12159
I	RNA annealing protein YRA1	protein	15	80% helix, 0% strand	Q12159
D, E, F	RNA (5'-R(PUPUPUPUPUPU)-3')	rna	6	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	763	0.85	0.88	104	ADP, BEF, MG
2	340	0.77	0.88	46	empty
3	227	0.73	0.88	39	ADP, BEF, MG
4	325	0.67	0.82	40	ADP, BEF, MG
5	209	0.59	0.81	28	empty

Interfaces

8 interfaces between chains.

B–C · 1125 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 643 Å² buried · 24 hydrogen bonds · protein-nucleic
A–C · 631 Å² buried · 6 hydrogen bonds · protein-protein
B–G · 625 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 623 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5SUP · Crystal structure of the Sub2-Yra1 complex in association with RNA · the same entry in another collection · chain F against F, TM-score 1.00
Q07478 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase SUB2 (Q07478) · a predicted model of the same protein · chain C against A, TM-score 0.99
Q12159 · AlphaFold monomer V2.0 prediction for RNA annealing protein YRA1 (Q12159) · a predicted model of the same protein · chain G against A, TM-score 0.61

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q07478
Every structure of UniProt Q12159
Elsewhere: RCSB PDB 5SUP · PDBe 5SUP · UniProt Q07478 · UniProt Q12159

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