MolNFT v1 · #104361 · protein

Ycao with non-hydrolyzable ATP (ampcpp) bound

4Q85 · Ribosomal protein S12 methylthiotransferase accessory…: “Ycao with non-hydrolyzable ATP (ampcpp) bound”. X-ray diffraction, 2 ligands (APC, MG), 20 pockets (best druggability 0.84). MolNFT v1 #104361 on GenesisL1: 3D structure…

PDB: 4Q85
Type: protein
Length: 4,527 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: APC, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	559	46% helix, 15% strand	P75838
B	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	573	46% helix, 14% strand	P75838
C	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	562	45% helix, 15% strand	P75838
D	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	572	45% helix, 14% strand	P75838
E	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	573	45% helix, 14% strand	P75838
F	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	570	45% helix, 15% strand	P75838
G	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	545	44% helix, 15% strand	P75838
H	Ribosomal protein S12 methylthiotransferase accessory factor ycao	protein	573	45% helix, 15% strand	P75838

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 5 copies · chains A, B, D, E, H
MG · Magnesium ion · metal · 19 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	410	0.84	0.92	36	empty
2	778	0.80	0.83	82	empty
3	1129	0.79	0.81	108	APC, MG
4	1058	0.79	0.80	117	APC
5	980	0.79	0.80	109	APC, MG

Interfaces

17 interfaces between chains.

A–B · 1622 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 1597 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1589 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1536 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 654 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4Q85 · YcaO with Non-hydrolyzable ATP (AMPCPP) 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 E 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 4Q85 · PDBe 4Q85 · UniProt P75838

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