Research workbench
Strep-tag ftra-P19 from rubrivivax gelatinosus in complex with copper and iron
Analyse Strep-tag ftra-P19 from rubrivivax gelatinosus in complex with copper and iron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R5P
- Type
- protein
- Length
- 933 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ftra-P19 protein
- Ligands
- CU1, MG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Ftra-P19 protein | protein | 156 | 4% helix, 49% strand | — |
| C | Ftra-P19 protein | protein | 154 | 4% helix, 50% strand | — |
| F | Ftra-P19 protein | protein | 155 | 4% helix, 50% strand | — |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.77 | 0.85 | 60 | empty |
| 2 | 1151 | 0.75 | 0.78 | 81 | MG |
| 3 | 336 | 0.66 | 0.81 | 32 | empty |
| 4 | 287 | 0.58 | 0.77 | 36 | empty |
| 5 | 202 | 0.53 | 0.78 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1896 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1889 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1871 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 583 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 573 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7R5P · Strep-tag FtrA-P19 from Rubrivivax gelatinosus in complex with copper and iron · 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
- Elsewhere: RCSB PDB 7R5P · PDBe 7R5P
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