MolNFT v1 · #140781 · protein
Zinc dependent alcohol dehydrogenase 2 from streptococcus pneumonia - apo form
5YLN · Alcohol dehydrogenase, zinc-containing: “Zinc dependent alcohol dehydrogenase 2 from streptococcus pneumonia - apo form”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #140781 on GenesisL1: 3D…
- PDB
- 5YLN
- Type
- protein
- Length
- 1,385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase, zinc-containing
- EC
- 1.1.1.1
- UniProt
- A0A0H2ZRI0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alcohol dehydrogenase, zinc-containing (EC 1.1.1.1) | protein | 348 | 32% helix, 26% strand | A0A0H2ZRI0 |
| B, D | Alcohol dehydrogenase, zinc-containing (EC 1.1.1.1) | protein | 346 | 31% helix, 26% strand | A0A0H2ZRI0 |
| C | Alcohol dehydrogenase, zinc-containing (EC 1.1.1.1) | protein | 345 | 32% helix, 25% strand | A0A0H2ZRI0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.78 | 0.83 | 71 | ZN, TRS |
| 2 | 697 | 0.78 | 0.82 | 86 | ZN, TRS |
| 3 | 725 | 0.77 | 0.81 | 79 | ZN, TRS |
| 4 | 606 | 0.75 | 0.82 | 71 | ZN, TRS |
| 5 | 569 | 0.68 | 0.78 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1835 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1814 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 681 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YLN · Zinc dependent alcohol dehydrogenase 2 from Streptococcus pneumonia - apo form · 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 A0A0H2ZRI0
- Elsewhere: RCSB PDB 5YLN · PDBe 5YLN · UniProt A0A0H2ZRI0
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