MolNFT v1 · #126855 · protein
Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)5
5MFF: “Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)5”. X-ray diffraction, 3 pockets (best druggability 0.89). MolNFT v1 #126855 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFF
- Type
- protein
- Length
- 1,138 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM5AII; (RR)5
- Pockets
- 3 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | YIIIM5AII | protein | 280 | 78% helix, 0% strand | — |
| C, D | YIIIM5AII | protein | 279 | 75% helix, 0% strand | — |
| E, F | (RR)5 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.89 | 0.90 | 130 | EDO |
| 2 | 810 | 0.85 | 0.88 | 93 | EDO |
| 3 | 722 | 0.83 | 0.87 | 79 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1169 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 919 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 708 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 682 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 676 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MFF · Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)5 · 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 5MFF · PDBe 5MFF
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