Research workbench
Crystal structure of a probable acyl CoA dehydrogenase from mycobacterium abscessus atcc 19977 / dsm 44196
Analyse Crystal structure of a probable acyl CoA dehydrogenase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R7K
- Type
- protein
- Length
- 1,509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable acyl CoA dehydrogenase
- UniProt
- B1MPB5
- Ligands
- FDA, K
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable acyl CoA dehydrogenase | protein | 378 | 56% helix, 17% strand | B1MPB5 |
| C | Probable acyl CoA dehydrogenase | protein | 377 | 55% helix, 16% strand | B1MPB5 |
| D | Probable acyl CoA dehydrogenase | protein | 376 | 56% helix, 17% strand | B1MPB5 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.87 | 99 | FDA, K |
| 2 | 1108 | 0.86 | 0.87 | 102 | FDA, K |
| 3 | 1039 | 0.86 | 0.86 | 93 | FDA, K |
| 4 | 1137 | 0.85 | 0.86 | 105 | FDA, K |
| 5 | 506 | 0.71 | 0.81 | 46 | K |
Interfaces
6 interfaces between chains.
- A–B · 1974 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1964 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1329 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1194 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3R7K · Crystal structure of a probable acyl CoA dehydrogenase from Mycobacterium abscessus ATCC… · 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 B1MPB5
- Elsewhere: RCSB PDB 3R7K · PDBe 3R7K · UniProt B1MPB5
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