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Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from unknown at 2.20 a resolution

Analyse Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CXT
Type: protein
Length: 1,098 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 39; Splicing factor U2AF 65 kda subunit
UniProt: Q8VH51, P26369
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 9 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, M	RNA-binding protein 39	protein	111	34% helix, 19% strand	Q8VH51
B	Splicing factor U2AF 65 kda subunit	protein	9	0% helix, 11% strand	P26369
C, G	RNA-binding protein 39	protein	112	34% helix, 19% strand	Q8VH51
D, H, J, L, N	Splicing factor U2AF 65 kda subunit	protein	11	0% helix, 9% strand	P26369
E, Q	RNA-binding protein 39	protein	112	34% helix, 20% strand	Q8VH51
F, R	Splicing factor U2AF 65 kda subunit	protein	10	0% helix, 10% strand	P26369
K	RNA-binding protein 39	protein	113	34% helix, 19% strand	Q8VH51
O	RNA-binding protein 39	protein	110	35% helix, 19% strand	Q8VH51
P	Splicing factor U2AF 65 kda subunit	protein	10	0% helix, 10% strand	P26369

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.61	0.74	50	empty
2	505	0.61	0.75	52	empty
3	503	0.61	0.75	53	empty
4	168	0.42	0.73	22	empty
5	123	0.40	0.74	23	empty

Interfaces

22 interfaces between chains.

C–D · 527 Å² buried · 11 hydrogen bonds · protein-protein
Q–R · 524 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 510 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 510 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 507 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5CXT · Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of… · 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 Q8VH51
Every structure of UniProt P26369
Elsewhere: RCSB PDB 5CXT · PDBe 5CXT · UniProt Q8VH51 · UniProt P26369

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