Research workbench
Archaeal branched-chain amino acid aminotransferase from archaeoglobus fulgidus; holoform
Analyse Archaeal branched-chain amino acid aminotransferase from archaeoglobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MQZ
- Type
- protein
- Length
- 1,723 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative branched-chain-amino-acid aminotransferase
- EC
- 2.6.1.42
- UniProt
- O29329
- Ligands
- TAM, CL
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Putative branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 287 | 31% helix, 30% strand | O29329 |
| B, C | Putative branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 286 | 30% helix, 30% strand | O29329 |
| D | Putative branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 290 | 29% helix, 29% strand | O29329 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, C, F, B, D, E
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.71 | 0.80 | 50 | EDO |
| 2 | 403 | 0.68 | 0.80 | 33 | empty |
| 3 | 402 | 0.68 | 0.80 | 49 | empty |
| 4 | 447 | 0.68 | 0.79 | 38 | empty |
| 5 | 390 | 0.67 | 0.80 | 32 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2434 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2410 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2391 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 827 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 822 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor).
Compared structures
- 5MQZ · Archaeal branched-chain amino acid aminotransferase from Archaeoglobus fulgidus; holoform · the same entry in another collection · chain F against F, TM-score 1.00
- O29329 · AlphaFold monomer V2.0 prediction for putative branched-chain-amino- acid… · a predicted model of the same protein · chain B 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 O29329
- Elsewhere: RCSB PDB 5MQZ · PDBe 5MQZ · UniProt O29329
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