MolNFT v1 · #136090 · protein
The crystal structure of an aminotransferase tlmj from streptoalloteichus hindustanus
5UID: “The crystal structure of an aminotransferase tlmj from streptoalloteichus hindustanus”. X-ray diffraction, 2 ligands (PLP, SO4), 12 pockets (best druggability 0.80). MolNFT v1 #136090 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UID
- Type
- protein
- Length
- 1,467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase tlmj
- UniProt
- A4KUD2
- Ligands
- PLP, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aminotransferase tlmj | protein | 367 | 43% helix, 17% strand | A4KUD2 |
| D | Aminotransferase tlmj | protein | 366 | 44% helix, 16% strand | A4KUD2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 25 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.80 | 0.96 | 35 | PLP |
| 2 | 147 | 0.80 | 0.97 | 38 | PLP |
| 3 | 486 | 0.70 | 0.80 | 40 | SO4 |
| 4 | 479 | 0.69 | 0.79 | 35 | SO4 |
| 5 | 460 | 0.68 | 0.79 | 32 | SO4 |
Interfaces
4 interfaces between chains.
- C–D · 2666 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2562 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered, cofactor).
Compared structures
- 5UID · The crystal structure of an aminotransferase TlmJ from Streptoalloteichus hindustanus · the same entry in another collection · chain A 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 A4KUD2
- Elsewhere: RCSB PDB 5UID · PDBe 5UID · UniProt A4KUD2
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