MolNFT v1 · #174588 · protein + RNA

Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-uaggu.

7C08 · Splicing factor U2AF 23 kda subunit: “Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-uaggu.”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #174588 on…

PDB: 7C08
Type: protein + RNA
Length: 2,188 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 · 13 distinct chains · 34% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, P	Splicing factor U2AF 23 kda subunit	protein	192	35% helix, 16% strand	Q09176
B	Splicing factor U2AF 59 kda subunit	protein	56	29% 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	35% helix, 17% strand	Q09176
E, T	Splicing factor U2AF 59 kda subunit	protein	50	20% helix, 2% strand	P36629
G, J	Splicing factor U2AF 23 kda subunit	protein	193	33% helix, 16% 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	28% helix, 2% strand	P36629
M	Splicing factor U2AF 23 kda subunit	protein	177	40% helix, 15% strand	Q09176
S	Splicing factor U2AF 23 kda subunit	protein	187	35% helix, 17% strand	Q09176
V	Splicing factor U2AF 23 kda subunit	protein	174	37% helix, 18% strand	Q09176
Y	Splicing factor U2AF 23 kda subunit	protein	178	38% helix, 17% strand	Q09176
Z	Splicing factor U2AF 59 kda subunit	protein	48	15% 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.87	0.89	115	empty
2	711	0.77	0.82	67	empty
3	746	0.67	0.75	70	empty
4	504	0.65	0.77	67	empty
5	422	0.62	0.77	54	empty

Interfaces

43 interfaces between chains.

V–W · 1768 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1720 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1699 Å² buried · 22 hydrogen bonds · protein-protein
M–N · 1675 Å² buried · 25 hydrogen bonds · protein-protein
S–T · 1674 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7C08 · Crystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA… · 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 7C08 · PDBe 7C08 · UniProt Q09176 · UniProt P36629

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