MolNFT v1 · #81860 · protein

Crystal structure of human RBM25

3V53 · RNA-binding protein 25: “Crystal structure of human RBM25”. X-ray diffraction, 8 pockets (best druggability 0.53). MolNFT v1 #81860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3V53
Type: protein
Length: 537 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 25
UniProt: P49756
Pockets: 8 · best druggability 0.53

Structure

x-ray diffraction · 5 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding protein 25	protein	110	74% helix, 0% strand	P49756
B	RNA-binding protein 25	protein	112	68% helix, 0% strand	P49756
C	RNA-binding protein 25	protein	104	71% helix, 0% strand	P49756
D	RNA-binding protein 25	protein	109	74% helix, 0% strand	P49756
E	RNA-binding protein 25	protein	102	67% helix, 0% strand	P49756

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	143	0.53	0.81	20	empty
2	138	0.52	0.80	20	empty
3	107	0.52	0.82	26	empty
4	74	0.48	0.83	20	empty
5	64	0.47	0.84	17	empty

Interfaces

5 interfaces between chains.

C–D · 572 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 515 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 99 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 34 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3V53 · Crystal structure of human RBM25 · the same entry in another collection · chain E against E, TM-score 1.00
P49756 · AlphaFold monomer V2.0 prediction for RNA-binding protein 25 (P49756) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P49756
Elsewhere: RCSB PDB 3V53 · PDBe 3V53 · UniProt P49756

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