MolNFT v1 · #126862 · protein
Designed armadillo repeat protein peptide fusion YIIIM6AII_GS11_(KR)5
5MFM: “Designed armadillo repeat protein peptide fusion YIIIM6AII_GS11_(KR)5”. X-ray diffraction, 2 ligands (CA, MG), 12 pockets (best druggability 0.85). MolNFT v1 #126862 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFM
- Type
- protein
- Length
- 2,086 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM6AII_GS11_(KR)5; Importin subunit alpha
- Ligands
- CA, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YIIIM6AII_GS11_(KR)5 | protein | 335 | 75% helix, 0% strand | — |
| B, D, E | YIIIM6AII_GS11_(KR)5 | protein | 333 | 75% helix, 0% strand | — |
| C | Importin subunit alpha | protein | 334 | 73% helix, 0% strand | — |
| F | YIIIM6AII_GS11_(KR)5 | protein | 334 | 75% helix, 0% strand | — |
| P, Q | YIIIM6AII_GS11_(KR)5 | protein | 42 | 48% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 23 copies · chains A, B, C, E, D, F
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, E, D, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.85 | 0.87 | 118 | empty |
| 2 | 1018 | 0.85 | 0.86 | 90 | empty |
| 3 | 1189 | 0.80 | 0.82 | 107 | CA |
| 4 | 240 | 0.70 | 0.86 | 32 | empty |
| 5 | 252 | 0.63 | 0.81 | 37 | empty |
Interfaces
14 interfaces between chains.
- D–F · 2158 Ų buried · 62 hydrogen bonds · protein-protein
- C–E · 2037 Ų buried · 53 hydrogen bonds · protein-protein
- C–Q · 964 Ų buried · 16 hydrogen bonds · protein-protein
- F–P · 849 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 524 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5MFM · Designed armadillo repeat protein peptide fusion YIIIM6AII_GS11_(KR)5 · the same entry in another collection · chain E against E, 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 5MFM · PDBe 5MFM
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