Research workbench
Crystal structure of P. abyssi SUA5 complexed with L-threonine
Analyse Crystal structure of P. abyssi SUA5 complexed with L-threonine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F8Y
- Type
- protein
- Length
- 1,361 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonylcarbamoyl-AMP synthase
- EC
- 2.7.7.87
- UniProt
- Q9UYB2
- Ligands
- THR
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Threonylcarbamoyl-AMP synthase (EC 2.7.7.87) | protein | 340 | 34% helix, 19% strand | Q9UYB2 |
| C | Threonylcarbamoyl-AMP synthase (EC 2.7.7.87) | protein | 341 | 33% helix, 20% strand | Q9UYB2 |
Ligands and binding sites
- THR · Threonine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.75 | 0.98 | 31 | THR |
| 2 | 91 | 0.75 | 0.97 | 31 | THR |
| 3 | 88 | 0.75 | 0.97 | 32 | THR |
| 4 | 66 | 0.74 | 0.99 | 29 | THR |
| 5 | 387 | 0.60 | 0.76 | 41 | empty |
Interfaces
2 interfaces between chains.
- B–D · 676 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6F8Y · Crystal structure of P. abyssi Sua5 complexed with L-threonine · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UYB2 · AlphaFold monomer V2.0 prediction for threonylcarbamoyl-AMP synthase (Q9UYB2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UYB2
- Elsewhere: RCSB PDB 6F8Y · PDBe 6F8Y · UniProt Q9UYB2
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