MolNFT v1 · #126854 · protein
Designed armadillo repeat protein YIIIM5AII in complex with (RR)4 peptide
5MFE: “Designed armadillo repeat protein YIIIM5AII in complex with (RR)4 peptide”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.81). MolNFT v1 #126854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFE
- Type
- protein
- Length
- 1,135 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM5AII; (RR)4
- Ligands
- CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YIIIM5AII | protein | 281 | 77% helix, 0% strand | — |
| B | YIIIM5AII | protein | 282 | 76% helix, 0% strand | — |
| C | YIIIM5AII | protein | 283 | 77% helix, 0% strand | — |
| D | YIIIM5AII | protein | 282 | 75% helix, 0% strand | — |
| E | (RR)4 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.81 | 0.84 | 92 | EDO |
| 2 | 867 | 0.74 | 0.79 | 55 | EDO |
| 3 | 418 | 0.73 | 0.83 | 47 | empty |
| 4 | 607 | 0.63 | 0.75 | 45 | empty |
| 5 | 286 | 0.53 | 0.75 | 24 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1494 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1475 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 774 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 679 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 112 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MFE · Designed armadillo repeat protein YIIIM5AII in complex with (RR)4 peptide · 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 5MFE · PDBe 5MFE
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