MolNFT v1 · #105387 · protein

The crystal structure of an apo RNA binding protein

4R3H · Yth domain-containing protein 1: “The crystal structure of an apo RNA binding protein”. X-ray diffraction, 2 ligands (UNX, SO4), 7 pockets (best druggability 0.44). MolNFT v1 #105387 on GenesisL1: 3D structure, binding sites and…

PDB: 4R3H
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein 1
UniProt: Q96MU7
Ligands: UNX, SO4
Pockets: 7 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing protein 1	protein	157	33% helix, 27% strand	Q96MU7
B	Yth domain-containing protein 1	protein	155	34% helix, 27% strand	Q96MU7

Ligands and binding sites

UNX · Unknown atom or ion · ion · 11 copies · chains A, B
SO4 · Sulfate ion · ion · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 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	74	0.44	0.80	18	empty
2	83	0.42	0.79	14	UNX
3	102	0.40	0.76	16	empty
4	91	0.37	0.75	16	empty
5	109	0.34	0.72	15	empty

Interfaces

1 interface between chains.

A–B · 260 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4R3H · The crystal structure of an apo RNA binding protein · the same entry in another collection · chain A against A, 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 Q96MU7
Elsewhere: RCSB PDB 4R3H · PDBe 4R3H · UniProt Q96MU7

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