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Crystal structure of yeast U2AF1 complex bound to 3' splice site RNA, 5'-uaggu.

Analyse Crystal structure of yeast U2AF1 complex bound to 3' splice site RNA, 5'-uaggu. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7C06
Type: protein + RNA
Length: 2,190 residues
Chains: 27
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Splicing factor U2AF 23 kda subunit; Splicing factor U2AF 59 kda subunit; RNA…
UniProt: Q09176, P36629
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 14 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, J	Splicing factor U2AF 23 kda subunit	protein	193	38% helix, 17% strand	Q09176
B	Splicing factor U2AF 59 kda subunit	protein	56	32% helix, 2% strand	P36629
C, F, I, L, O, R, U, X, 1	RNA (5'-R(UUPAPGPGPU)-3')	rna	5	—	—
D	Splicing factor U2AF 23 kda subunit	protein	187	39% helix, 17% strand	Q09176
E	Splicing factor U2AF 59 kda subunit	protein	51	25% helix, 2% strand	P36629
G, P	Splicing factor U2AF 23 kda subunit	protein	192	39% helix, 14% strand	Q09176
H, N, Q, W	Splicing factor U2AF 59 kda subunit	protein	53	32% helix, 2% strand	P36629
K	Splicing factor U2AF 59 kda subunit	protein	54	31% helix, 2% strand	P36629
M	Splicing factor U2AF 23 kda subunit	protein	178	43% helix, 15% strand	Q09176
S	Splicing factor U2AF 23 kda subunit	protein	186	38% helix, 17% strand	Q09176
T	Splicing factor U2AF 59 kda subunit	protein	50	32% helix, 2% strand	P36629
V	Splicing factor U2AF 23 kda subunit	protein	174	38% helix, 18% strand	Q09176
Y	Splicing factor U2AF 23 kda subunit	protein	179	44% helix, 17% strand	Q09176
Z	Splicing factor U2AF 59 kda subunit	protein	48	31% helix, 2% strand	P36629

Ligands and binding sites

ZN · Zinc ion · metal · 18 copies · chains A, C, D, F, G, I, J, L, M, O, P, R, S, U, V, X, Y, 1

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.87	0.89	118	empty
2	672	0.77	0.82	69	empty
3	622	0.65	0.75	59	empty
4	374	0.60	0.76	58	empty
5	304	0.59	0.78	41	empty

Interfaces

42 interfaces between chains.

A–B · 1702 Å² buried · 23 hydrogen bonds · protein-protein
V–W · 1693 Å² buried · 22 hydrogen bonds · protein-protein
M–N · 1692 Å² buried · 25 hydrogen bonds · protein-protein
Y–Z · 1692 Å² buried · 22 hydrogen bonds · protein-protein
G–H · 1683 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7C06 · Crystal structure of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU. · the same entry in another collection · chain K against K, TM-score 1.00

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 Q09176
Every structure of UniProt P36629
Elsewhere: RCSB PDB 7C06 · PDBe 7C06 · UniProt Q09176 · UniProt P36629

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