Research workbench
Crystal structure of thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TSAB2D2E2 bound to ATP and carboxy-AMP
Analyse Crystal structure of thermotoga maritima threonylcarbamoyladenosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N9A
- Type
- protein
- Length
- 702 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA threonylcarbamoyladenosine biosynthesis protein tsab; TRNA N6-adenosine…
- EC
- 2.3.1.234
- UniProt
- Q9WZX7, Q9WXZ2, Q9X1W7
- Ligands
- AE3, KG4, ADP, ATP, ZN, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 211 | 34% helix, 29% strand | Q9WZX7 |
| D | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) | protein | 330 | 45% helix, 18% strand | Q9WXZ2 |
| E | TRNA threonylcarbamoyladenosine biosynthesis protein tsae | protein | 161 | 37% helix, 30% strand | Q9X1W7 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains B
- KG4 · 5'-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine · ligand · chains D, E
- ADP · Adenosine-5'-diphosphate · ligand · chains D
- ATP · Adenosine-5'-triphosphate · ligand · chains D, E
- ZN · Zinc ion · metal · chains D
- MG · Magnesium ion · metal · chains D, E
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.77 | 0.82 | 66 | KG4 |
| 2 | 358 | 0.68 | 0.82 | 44 | ATP, MG |
| 3 | 471 | 0.65 | 0.77 | 42 | empty |
| 4 | 123 | 0.62 | 0.86 | 32 | empty |
| 5 | 114 | 0.48 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1242 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1171 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 808 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6N9A · Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9WZX7 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain B against A, TM-score 0.92
- Q9WXZ2 · AlphaFold monomer V2.0 prediction for tRNA N6-adenosine threonylcarbamoyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.89
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 Q9WZX7
- Every structure of UniProt Q9WXZ2
- Every structure of UniProt Q9X1W7
- Elsewhere: RCSB PDB 6N9A · PDBe 6N9A · UniProt Q9WZX7 · UniProt Q9WXZ2 · UniProt Q9X1W7
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