MolNFT v1 · #148492 · protein
Crystal structure of P. abyssi SUA5 complexed with L-threonine and ppi
6F87 · Threonylcarbamoyl-AMP synthase: “Crystal structure of P. abyssi SUA5 complexed with L-threonine and ppi”. X-ray diffraction, 2 ligands (POP, THR), 12 pockets (best druggability 0.73). MolNFT v1 #148492 on GenesisL1: 3D structure…
- PDB
- 6F87
- Type
- protein
- Length
- 1,360 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
- POP, THR
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Threonylcarbamoyl-AMP synthase (EC 2.7.7.87) | protein | 340 | 35% helix, 20% strand | Q9UYB2 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.73 | 0.95 | 33 | POP, THR |
| 2 | 91 | 0.72 | 0.95 | 35 | POP, THR |
| 3 | 75 | 0.72 | 0.97 | 28 | POP, THR |
| 4 | 81 | 0.72 | 0.96 | 34 | POP, THR |
| 5 | 417 | 0.58 | 0.75 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–C · 587 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 532 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 111 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6F87 · Crystal structure of P. abyssi Sua5 complexed with L-threonine and PPi · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UYB2 · AlphaFold monomer V2.0 prediction for threonylcarbamoyl-AMP synthase (Q9UYB2) · a predicted model of the same protein · chain D 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 6F87 · PDBe 6F87 · UniProt Q9UYB2
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