Research workbench
Crystal structure of a probable oxidoreductase from Mycobacterium abscessus solved by iodide ion SAD
Analyse Crystal structure of a probable oxidoreductase from Mycobacterium abscessus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EYE
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Mycobacterium abscessus
- Molecule
- Probable oxidoreductase
- UniProt
- B1ML27
- Ligands
- IOD
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable oxidoreductase | protein | 313 | 34% helix, 28% strand | B1ML27 |
| B | Probable oxidoreductase | protein | 309 | 35% helix, 29% strand | B1ML27 |
Ligands and binding sites
- IOD · Iodide ion · ion · 18 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.67 | 0.77 | 52 | MPD, IOD |
| 2 | 497 | 0.66 | 0.77 | 51 | MPD, IOD |
| 3 | 510 | 0.63 | 0.76 | 47 | empty |
| 4 | 68 | 0.62 | 0.91 | 22 | empty |
| 5 | 431 | 0.61 | 0.76 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4EYE · Crystal structure of a probable oxidoreductase from mycobacterium abscessus solved by… · 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 B1ML27
- Elsewhere: RCSB PDB 4EYE · PDBe 4EYE · UniProt B1ML27
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