Research workbench
Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with D-kdg
Analyse Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W3N
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxy gluconate aldolase
- EC
- 4.1.2.20
- UniProt
- O54288
- Ligands
- SSH
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-keto-3-deoxy gluconate aldolase (EC 4.1.2.20) | protein | 293 | 53% helix, 14% strand | O54288 |
Ligands and binding sites
- SSH · 3-deoxy-D-arabino-hexonic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.77 | 0.89 | 39 | SSH, GOL |
| 2 | 318 | 0.77 | 0.88 | 39 | SSH, GOL |
| 3 | 285 | 0.74 | 0.88 | 36 | empty |
| 4 | 330 | 0.74 | 0.86 | 38 | SSH |
| 5 | 331 | 0.74 | 0.85 | 37 | SSH, GOL |
Interfaces
4 interfaces between chains.
- B–C · 1707 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1655 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1143 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1140 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 1W3N · Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDG · the same entry in another collection · chain A against A, TM-score 1.00
- O54288 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy… · 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 O54288
- Elsewhere: RCSB PDB 1W3N · PDBe 1W3N · UniProt O54288
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