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Engineered plp-dependent decarboxylative aldolase from aspergillus flavus, USTD2.0, bound as the internal aldimine
Analyse Engineered plp-dependent decarboxylative aldolase from aspergillus flavus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MKV
- Type
- protein
- Length
- 1,220 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase-like protein ustd
- EC
- 2.-.-.-
- UniProt
- B8NM72
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine desulfurase-like protein ustd (EC 2.-.-.-) | protein | 407 | 44% helix, 17% strand | B8NM72 |
| C | Cysteine desulfurase-like protein ustd (EC 2.-.-.-) | protein | 406 | 44% helix, 17% strand | B8NM72 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.77 | 0.83 | 65 | empty |
| 2 | 91 | 0.71 | 0.94 | 32 | empty |
| 3 | 274 | 0.67 | 0.83 | 28 | empty |
| 4 | 334 | 0.57 | 0.76 | 40 | empty |
| 5 | 331 | 0.56 | 0.76 | 40 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2832 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor, oxidation).
Compared structures
- 7MKV · Engineered PLP-dependent decarboxylative aldolase from Aspergillus flavus, UstD2.0, bound… · the same entry in another collection · chain A against A, TM-score 1.00
- B8NM72 · AlphaFold monomer V2.0 prediction for cysteine desulfurase-like protein ustd (B8NM72) · 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 B8NM72
- Elsewhere: RCSB PDB 7MKV · PDBe 7MKV · UniProt B8NM72
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