MolNFT v1 · #79475 · protein
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia ambifaria
3T4C · 2-dehydro-3-deoxyphosphooctonate aldolase 1: “Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia ambifaria”. X-ray diffraction, 15 pockets (best druggability 0.62). MolNFT v1 #79475 on GenesisL1: 3D…
- PDB
- 3T4C
- Type
- protein
- Length
- 1,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase 1
- EC
- 2.5.1.55
- UniProt
- B1YT10
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase 1 (EC 2.5.1.55) | protein | 264 | 42% helix, 19% strand | B1YT10 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase 1 (EC 2.5.1.55) | protein | 262 | 45% helix, 19% strand | B1YT10 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase 1 (EC 2.5.1.55) | protein | 262 | 44% helix, 19% strand | B1YT10 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase 1 (EC 2.5.1.55) | protein | 259 | 44% helix, 19% strand | B1YT10 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.62 | 0.79 | 44 | empty |
| 2 | 231 | 0.53 | 0.77 | 32 | empty |
| 3 | 254 | 0.53 | 0.76 | 41 | empty |
| 4 | 80 | 0.53 | 0.85 | 16 | empty |
| 5 | 89 | 0.51 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1651 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1538 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 863 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 793 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 216 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3T4C · Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria · 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 B1YT10
- Elsewhere: RCSB PDB 3T4C · PDBe 3T4C · UniProt B1YT10
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