Research workbench
Crystal structure of lnmf protein from streptomyces amphibiosporus
Analyse Crystal structure of lnmf protein from streptomyces amphibiosporus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NNQ
- Type
- protein
- Length
- 687 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative enoyl-CoA hydratase
- UniProt
- Q8GGP6
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative enoyl-CoA hydratase | protein | 228 | 50% helix, 19% strand | Q8GGP6 |
| B | Putative enoyl-CoA hydratase | protein | 230 | 50% helix, 19% strand | Q8GGP6 |
| C | Putative enoyl-CoA hydratase | protein | 229 | 50% helix, 18% strand | Q8GGP6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.77 | 0.84 | 70 | SO4 |
| 2 | 127 | 0.76 | 0.95 | 25 | empty |
| 3 | 72 | 0.68 | 0.95 | 18 | empty |
| 4 | 247 | 0.65 | 0.83 | 22 | empty |
| 5 | 70 | 0.65 | 0.93 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1417 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1411 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4NNQ · Crystal structure of LnmF protein from Streptomyces amphibiosporus · 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 Q8GGP6
- Elsewhere: RCSB PDB 4NNQ · PDBe 4NNQ · UniProt Q8GGP6
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