Research workbench
Crystal structure of probable oxidoreductase protein from rhizobium etli cfn 42
Analyse Crystal structure of probable oxidoreductase protein from rhizobium etli cfn 42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAD
- Type
- protein
- Length
- 1,266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable oxidoreductase protein
- UniProt
- Q2KDJ1
- Ligands
- NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable oxidoreductase protein | protein | 317 | 38% helix, 29% strand | Q2KDJ1 |
| B, D | Probable oxidoreductase protein | protein | 316 | 39% helix, 29% strand | Q2KDJ1 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.84 | 0.85 | 68 | empty |
| 2 | 251 | 0.83 | 0.96 | 30 | empty |
| 3 | 241 | 0.83 | 0.95 | 28 | empty |
| 4 | 50 | 0.65 | 0.95 | 15 | empty |
| 5 | 484 | 0.62 | 0.76 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1621 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1617 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4HAD · Crystal structure of probable oxidoreductase protein from Rhizobium etli CFN 42 · 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 Q2KDJ1
- Elsewhere: RCSB PDB 4HAD · PDBe 4HAD · UniProt Q2KDJ1
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