MolNFT v1 · #57864 · protein

Crystal structure of human TYW5

3AL5 · Jmjc domain-containing protein C2ORF60: “Crystal structure of human TYW5”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.71). MolNFT v1 #57864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3AL5
Type: protein
Length: 1,205 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Jmjc domain-containing protein C2ORF60
UniProt: A2RUC4
Ligands: MG
Pockets: 15 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Jmjc domain-containing protein C2ORF60	protein	302	30% helix, 25% strand	A2RUC4
B	Jmjc domain-containing protein C2ORF60	protein	311	31% helix, 26% strand	A2RUC4
C	Jmjc domain-containing protein C2ORF60	protein	284	29% helix, 25% strand	A2RUC4
D	Jmjc domain-containing protein C2ORF60	protein	308	30% helix, 28% strand	A2RUC4

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, D

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	429	0.71	0.82	50	empty
2	319	0.68	0.83	54	empty
3	240	0.67	0.84	40	MG
4	248	0.63	0.82	40	empty
5	86	0.61	0.88	17	empty

Interfaces

2 interfaces between chains.

C–D · 2545 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2463 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3AL5 · Crystal structure of Human TYW5 · the same entry in another collection · chain D against D, TM-score 1.00
A2RUC4 · AlphaFold monomer V2.0 prediction for tRNA wybutosine-synthesizing protein 5 (A2RUC4) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 A2RUC4
Elsewhere: RCSB PDB 3AL5 · PDBe 3AL5 · UniProt A2RUC4

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