MolNFT v1 · #156740 · protein
Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from legionella pneumophila philadelphia 1
6MDY: “Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from legionella pneumophila philadelphia 1”. X-ray diffraction, 12 pockets (best druggability 0.64). MolNFT v1 #156740 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MDY
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- Q5ZWA3
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 242 | 41% helix, 21% strand | Q5ZWA3 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 242 | 43% helix, 21% strand | Q5ZWA3 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 239 | 42% helix, 21% strand | Q5ZWA3 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 255 | 41% helix, 20% strand | Q5ZWA3 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.64 | 0.79 | 54 | empty |
| 2 | 296 | 0.57 | 0.77 | 37 | empty |
| 3 | 328 | 0.57 | 0.76 | 36 | empty |
| 4 | 279 | 0.57 | 0.77 | 36 | empty |
| 5 | 79 | 0.45 | 0.81 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1252 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1198 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1105 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 859 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 212 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MDY · Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5ZWA3 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (Q5ZWA3) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q5ZWA3
- Elsewhere: RCSB PDB 6MDY · PDBe 6MDY · UniProt Q5ZWA3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.