Research workbench
Crystal structure of a dimeric ferredoxin-like protein (JCVI_PEP_1096682647733) from uncultured marine organism at 1.85 a resolution
Analyse Crystal structure of a dimeric ferredoxin-like protein (JCVI_PEP_1096682647733)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OD6
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- Ligands
- OHA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 110 | 39% helix, 35% strand | — |
| B, D | Hypothetical protein | protein | 108 | 43% helix, 36% strand | — |
| C | Hypothetical protein | protein | 107 | 42% helix, 36% strand | — |
Ligands and binding sites
- OHA · 10-oxohexadecanoic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.68 | 0.79 | 36 | OHA |
| 2 | 241 | 0.65 | 0.82 | 25 | OHA |
| 3 | 275 | 0.64 | 0.81 | 31 | OHA |
| 4 | 381 | 0.63 | 0.77 | 30 | OHA |
| 5 | 133 | 0.48 | 0.78 | 20 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1524 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1521 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 146 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 2OD6 · Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) 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
- Elsewhere: RCSB PDB 2OD6 · PDBe 2OD6
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