MolNFT v1 · #83225 · protein + RNA

Crystal structure of protein-RNA complex

3WBM · DNA/RNA-binding protein alba 1: “Crystal structure of protein-RNA complex”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #83225 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WBM
Type: protein + RNA
Length: 395 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA-binding protein alba 1; RNA (25-mer)
UniProt: P60848
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA/RNA-binding protein alba 1	protein	86	34% helix, 41% strand	P60848
B	DNA/RNA-binding protein alba 1	protein	84	35% helix, 39% strand	P60848
D	DNA/RNA-binding protein alba 1	protein	89	35% helix, 42% strand	P60848
X, Y	RNA (25-mer)	rna	25	—	—

Pockets

5 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	1015	0.77	0.79	97	empty
2	887	0.71	0.77	47	empty
3	917	0.67	0.74	49	empty
4	77	0.42	0.80	21	empty
5	74	0.36	0.77	15	empty

Interfaces

13 interfaces between chains.

X–Y · 1110 Å² buried · 111 hydrogen bonds · nucleic-nucleic
A–B · 796 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 747 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 533 Å² buried · 7 hydrogen bonds · protein-protein
A–X · 418 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

3WBM · Crystal Structure of protein-RNA complex · the same entry in another collection · chain Y against Y, TM-score 1.00
P60848 · AlphaFold monomer V2.0 prediction for DNA/RNA-binding protein alba 1 (P60848) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P60848
Elsewhere: RCSB PDB 3WBM · PDBe 3WBM · UniProt P60848

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