MolNFT v1 · #28418 · protein
Crystal structure of the bacillis subtilis hmg-CoA lyase, northeast structural genomics target SR181.
1YDO: “Crystal structure of the bacillis subtilis hmg-CoA lyase, northeast structural genomics target SR181.”. X-ray diffraction, 1 ligand (IOD), 13 pockets (best druggability 0.84). MolNFT v1 #28418 on GenesisL1: 3D structure, binding…
- PDB
- 1YDO
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmg-CoA lyase
- UniProt
- O34873
- Ligands
- IOD
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hmg-CoA lyase | protein | 298 | 47% helix, 19% strand | O34873 |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.84 | 0.89 | 88 | empty |
| 2 | 300 | 0.78 | 0.90 | 41 | empty |
| 3 | 358 | 0.75 | 0.86 | 41 | empty |
| 4 | 72 | 0.75 | 0.98 | 31 | empty |
| 5 | 67 | 0.74 | 0.98 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1367 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1327 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 423 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 1YDO · Crystal Structure of the Bacillis subtilis HMG-CoA Lyase, Northeast Structural Genomics… · the same entry in another collection · chain A against A, TM-score 1.00
- O34873 · AlphaFold monomer V2.0 prediction for hydroxymethylglutaryl-CoA lyase yngg (O34873) · 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 O34873
- Elsewhere: RCSB PDB 1YDO · PDBe 1YDO · UniProt O34873
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