Research workbench
Mbnp from methylosinus trichosporium
Analyse Mbnp from methylosinus trichosporium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L6G
- Type
- protein
- Length
- 1,743 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-mystery pair system four-cys motif protein
- UniProt
- A0A2D2CY67
- Ligands
- CU, CA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-mystery pair system four-cys motif protein | protein | 293 | 6% helix, 44% strand | A0A2D2CY67 |
| B | Metallo-mystery pair system four-cys motif protein | protein | 289 | 6% helix, 44% strand | A0A2D2CY67 |
| C | Metallo-mystery pair system four-cys motif protein | protein | 288 | 6% helix, 45% strand | A0A2D2CY67 |
| D | Metallo-mystery pair system four-cys motif protein | protein | 287 | 6% helix, 43% strand | A0A2D2CY67 |
| E | Metallo-mystery pair system four-cys motif protein | protein | 295 | 6% helix, 43% strand | A0A2D2CY67 |
| F | Metallo-mystery pair system four-cys motif protein | protein | 291 | 5% helix, 44% strand | A0A2D2CY67 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 19 copies · chains A, E, B, F, C, D
- EDO · 1,2-ethanediol · additive · 36 copies · chains A, E, B, F, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.81 | 0.82 | 113 | CU, SO4, EDO |
| 2 | 996 | 0.79 | 0.81 | 91 | EDO |
| 3 | 696 | 0.77 | 0.83 | 66 | EDO, SO4 |
| 4 | 223 | 0.48 | 0.75 | 29 | EDO |
| 5 | 137 | 0.48 | 0.78 | 20 | SO4 |
Interfaces
9 interfaces between chains.
- A–E · 815 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 792 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 724 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 383 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 275 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 modified (disulfide, nonstandard).
Compared structures
- 7L6G · MbnP from Methylosinus trichosporium · 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 A0A2D2CY67
- Elsewhere: RCSB PDB 7L6G · PDBe 7L6G · UniProt A0A2D2CY67
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