Research workbench
Crystal structure of the N-terminal domain of an uncharacterized protein (WS1339) from wolinella succinogenes
Analyse Crystal structure of the N-terminal domain of an uncharacterized protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HDG
- Type
- protein
- Length
- 495 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q7MRH8
- Ligands
- MG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Uncharacterized protein | protein | 124 | 49% helix, 15% strand | Q7MRH8 |
| B | Uncharacterized protein | protein | 123 | 47% helix, 16% strand | Q7MRH8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.63 | 0.82 | 38 | empty |
| 2 | 287 | 0.55 | 0.76 | 33 | empty |
| 3 | 286 | 0.54 | 0.75 | 28 | empty |
| 4 | 71 | 0.34 | 0.76 | 14 | empty |
| 5 | 68 | 0.28 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 849 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 401 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3HDG · Crystal structure of the N-terminal domain of an uncharacterized protein (WS1339) from… · 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 Q7MRH8
- Elsewhere: RCSB PDB 3HDG · PDBe 3HDG · UniProt Q7MRH8
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