Research workbench
Crystal structure of E. COLI periplasmic protein hdea
Analyse Crystal structure of E. COLI periplasmic protein hdea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJ8
- Type
- protein
- Length
- 474 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hns-dependent expression a
- UniProt
- P26604
- Pockets
- 11 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein hns-dependent expression a | protein | 79 | 66% helix, 3% strand | P26604 |
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.45 | 0.81 | 24 | empty |
| 2 | 144 | 0.45 | 0.76 | 20 | empty |
| 3 | 152 | 0.43 | 0.75 | 22 | empty |
| 4 | 88 | 0.40 | 0.78 | 13 | empty |
| 5 | 99 | 0.39 | 0.76 | 26 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1243 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1207 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1172 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 401 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1DJ8 · Crystal structure of E. COLI periplasmic protein hdea · 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 P26604
- Elsewhere: RCSB PDB 1DJ8 · PDBe 1DJ8 · UniProt P26604
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