MolNFT v1 · #171518 · protein
Tsabd bound to the inhibitor
6Z81 · TRNA N6-adenosine threonylcarbamoyltransferase: “Tsabd bound to the inhibitor”. X-ray diffraction, 6 ligands (QCB, AMP, NI), 10 pockets (best druggability 0.75). MolNFT v1 #171518 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Z81
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA N6-adenosine threonylcarbamoyltransferase; TRNA threonylcarbamoyladenosine…
- EC
- 2.3.1.234
- UniProt
- P05852, P76256
- Ligands
- QCB, AMP, NI, NA, ZN, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) | protein | 342 | 46% helix, 20% strand | P05852 |
| B | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) | protein | 341 | 46% helix, 20% strand | P05852 |
| C | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 229 | 36% helix, 28% strand | P76256 |
| D | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 228 | 36% helix, 27% strand | P76256 |
Ligands and binding sites
- QCB · (2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.75 | 0.79 | 80 | QCB, SO4 |
| 2 | 789 | 0.75 | 0.80 | 86 | ZN, QCB, AMP |
| 3 | 340 | 0.65 | 0.80 | 43 | empty |
| 4 | 277 | 0.56 | 0.77 | 31 | empty |
| 5 | 229 | 0.56 | 0.78 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1429 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1419 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 812 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6Z81 · TsaBD bound to the inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P05852 · AlphaFold monomer V2.0 prediction for tRNA N6-adenosine threonylcarbamoyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P76256 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P05852
- Every structure of UniProt P76256
- Elsewhere: RCSB PDB 6Z81 · PDBe 6Z81 · UniProt P05852 · UniProt P76256
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