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Ycao with AMP bound

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

PDB: 4Q86
Type: protein
Length: 4,627 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein S12 methylthiotransferase accessory factor ycao
UniProt: P75838
Ligands: AMP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	582	45% helix, 15% strand	P75838
B, H	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	583	45% helix, 15% strand	P75838
C	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	570	46% helix, 15% strand	P75838
E	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	578	45% helix, 15% strand	P75838
F	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	574	45% helix, 15% strand	P75838
G	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	575	45% helix, 15% strand	P75838

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 7 copies · chains A, B, C, D, E, G, H
MG · Magnesium ion · metal · 21 copies · chains A, B, C, D, E, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	544	0.81	0.87	62	empty
2	987	0.79	0.81	115	AMP, MG
3	953	0.79	0.81	102	AMP, MG
4	958	0.79	0.81	106	AMP, MG
5	1002	0.79	0.80	107	AMP, MG

Interfaces

15 interfaces between chains.

E–F · 1619 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 1616 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1603 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1591 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 647 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4Q86 · YcaO with AMP Bound · the same entry in another collection · chain H against H, TM-score 1.00
P75838 · AlphaFold monomer V2.0 prediction for ribosomal protein S12 methylthiotransferase… · a predicted model of the same protein · chain G 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 P75838
Elsewhere: RCSB PDB 4Q86 · PDBe 4Q86 · UniProt P75838

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