MolNFT v1 · #122492 · protein

Crystal structure of the human RBM7 rrm domain

5IQQ · RNA-binding protein 7: “Crystal structure of the human RBM7 rrm domain”. X-ray diffraction, 5 pockets (best druggability 0.40). MolNFT v1 #122492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IQQ
Type: protein
Length: 405 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 7
UniProt: Q9Y580
Pockets: 5 · best druggability 0.40

Structure

x-ray diffraction · 5 distinct chains · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding protein 7	protein	83	24% helix, 30% strand	Q9Y580
B	RNA-binding protein 7	protein	78	26% helix, 31% strand	Q9Y580
C	RNA-binding protein 7	protein	83	25% helix, 27% strand	Q9Y580
D	RNA-binding protein 7	protein	81	25% helix, 32% strand	Q9Y580
E	RNA-binding protein 7	protein	80	25% helix, 30% strand	Q9Y580

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.40	0.77	15	empty
2	74	0.37	0.77	12	empty
3	75	0.35	0.75	12	empty
4	60	0.33	0.76	11	empty
5	61	0.32	0.75	15	empty

Interfaces

5 interfaces between chains.

D–E · 336 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 302 Å² buried · 1 hydrogen bond · protein-protein
C–D · 275 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 273 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 273 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5IQQ · Crystal structure of the human RBM7 RRM domain · the same entry in another collection · chain E against E, TM-score 1.00
Q9Y580 · AlphaFold monomer V2.0 prediction for RNA-binding protein 7 (Q9Y580) · a predicted model of the same protein · chain E 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 Q9Y580
Elsewhere: RCSB PDB 5IQQ · PDBe 5IQQ · UniProt Q9Y580

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