Research workbench
Ycao with non-hydrolyzable ATP (ampcpp) bound
Analyse Ycao with non-hydrolyzable ATP (ampcpp) bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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.
| Volume (ų) | 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 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1597 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1589 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1536 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 654 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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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