Research workbench
Structure of the periplasmic domain of doti (crystal form I)
Analyse Structure of the periplasmic domain of doti (crystal form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WZ4
- Type
- protein
- Length
- 1,103 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Doti
- UniProt
- O54626
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Doti | protein | 137 | 33% helix, 41% strand | O54626 |
| C, E, H | Doti | protein | 139 | 32% helix, 42% strand | O54626 |
| D, F | Doti | protein | 136 | 33% helix, 43% strand | O54626 |
| G | Doti | protein | 140 | 32% helix, 40% strand | O54626 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 16 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.66 | 0.86 | 19 | MRD, MPD |
| 2 | 254 | 0.65 | 0.82 | 38 | MRD, MPD |
| 3 | 276 | 0.65 | 0.81 | 32 | MRD, MPD |
| 4 | 261 | 0.65 | 0.82 | 35 | MRD, MPD |
| 5 | 172 | 0.63 | 0.84 | 27 | MRD, MPD |
Interfaces
13 interfaces between chains.
- G–H · 813 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 801 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 800 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 782 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 778 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3WZ4 · Structure of the periplasmic domain of DotI (crystal form I) · 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 O54626
- Elsewhere: RCSB PDB 3WZ4 · PDBe 3WZ4 · UniProt O54626
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