Research workbench
Crystal structure of 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from pseudomonas aeruginosa.
Analyse Crystal structure of 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LU0
- Type
- protein
- Length
- 996 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
- Q9ZFK4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 247 | 41% helix, 21% strand | Q9ZFK4 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 247 | 41% helix, 21% strand | Q9ZFK4 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 250 | 42% helix, 21% strand | Q9ZFK4 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 252 | 38% helix, 21% strand | Q9ZFK4 |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.64 | 0.82 | 36 | empty |
| 2 | 366 | 0.64 | 0.79 | 36 | empty |
| 3 | 355 | 0.62 | 0.78 | 36 | empty |
| 4 | 315 | 0.62 | 0.79 | 41 | empty |
| 5 | 229 | 0.53 | 0.77 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1559 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1502 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1203 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 1128 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 221 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4LU0 · Crystal structure of 2-Keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ZFK4 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (Q9ZFK4) · a predicted model of the same protein · chain C 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 Q9ZFK4
- Elsewhere: RCSB PDB 4LU0 · PDBe 4LU0 · UniProt Q9ZFK4
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