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APO YCAO

Analyse APO YCAO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q84
Type: protein
Length: 1,141 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein S12 methylthiotransferase accessory factor ycao
UniProt: P75838
Ligands: HG
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	568	45% helix, 14% strand	P75838
B	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	573	45% helix, 14% strand	P75838

Ligands and binding sites

HG · Mercury (II) ion · metal · 4 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.76	0.79	99	HG
2	991	0.75	0.78	94	empty
3	150	0.42	0.74	27	empty
4	79	0.34	0.75	16	empty
5	77	0.32	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1587 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4Q84 · Apo YcaO · the same entry in another collection · chain A against A, TM-score 1.00
P75838 · AlphaFold monomer V2.0 prediction for ribosomal protein S12 methylthiotransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P75838
Elsewhere: RCSB PDB 4Q84 · PDBe 4Q84 · UniProt P75838

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