Research workbench
TarP-3RboP
Analyse TarP-3RboP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4F
- Type
- protein
- Length
- 3,773 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.18
- Source
- Staphylococcus aureus (strain N315)
- Molecule
- Probable ss-1,3-N-acetylglucosaminyltransferase
- UniProt
- A0A0H3JNB0
- Ligands
- FQ8, MG, CL
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.18 · 9 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, H | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 318 | 45% helix, 14% strand | A0A0H3JNB0 |
| C, G, D | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 314 | 46% helix, 14% strand | A0A0H3JNB0 |
| F | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 315 | 46% helix, 14% strand | A0A0H3JNB0 |
| O | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 316 | 45% helix, 14% strand | A0A0H3JNB0 |
| P | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 307 | 46% helix, 14% strand | A0A0H3JNB0 |
| E | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 317 | 45% helix, 15% strand | A0A0H3JNB0 |
| Q | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 312 | 45% helix, 15% strand | A0A0H3JNB0 |
| A | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 317 | 45% helix, 15% strand | A0A0H3JNB0 |
| I | Probable ss-1,3-N-acetylglucosaminyltransferase | protein | 311 | 46% helix, 15% strand | A0A0H3JNB0 |
Ligands and binding sites
- FQ8 · [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] [(2~{R},3~{R},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentoxy]phosphoryl]oxy-pentyl] hydrogen phosphate · ligand · 12 copies · chains B, C, F, O, P, E, G, Q, A, D, H, I
- MG · Magnesium ion · metal · 4 copies · chains B, C, F, E, G, Q, A, D, H, I
- CL · Chloride ion · ion · 17 copies · chains B, E, C, F, O, G, Q, A, H, D, I
- GOL · Glycerol · additive · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.63 | 0.85 | 22 | empty |
| 2 | 121 | 0.63 | 0.87 | 22 | empty |
| 3 | 113 | 0.63 | 0.88 | 19 | empty |
| 4 | 266 | 0.62 | 0.80 | 38 | empty |
| 5 | 104 | 0.61 | 0.87 | 18 | empty |
Interfaces
21 interfaces between chains.
- A–H · 567 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 551 Ų buried · 3 hydrogen bonds · protein-protein
- O–H · 551 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 530 Ų buried · 3 hydrogen bonds · protein-protein
- E–Q · 529 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6H4F · TARP-3RBOP · the same entry in another collection · chain A 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 A0A0H3JNB0
- Elsewhere: RCSB PDB 6H4F · PDBe 6H4F · UniProt A0A0H3JNB0
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