Research workbench
Designed armadillo repeat protein YIIIM3AIII
Analyse Designed armadillo repeat protein YIIIM3AIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MFO
- Type
- protein
- Length
- 1,194 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM3AIII
- Ligands
- CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | YIIIM3AIII | protein | 199 | 76% helix, 0% strand | — |
| B | YIIIM3AIII | protein | 198 | 75% helix, 0% strand | — |
| D | YIIIM3AIII | protein | 200 | 73% helix, 0% strand | — |
| E | YIIIM3AIII | protein | 197 | 75% helix, 0% strand | — |
| F | YIIIM3AIII | protein | 201 | 72% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 19 copies · chains A, B, D, E, C, F
- EDO · 1,2-ethanediol · additive · chains F
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 | 1058 | 0.81 | 0.82 | 110 | CA |
| 2 | 497 | 0.71 | 0.81 | 66 | CA |
| 3 | 399 | 0.59 | 0.76 | 38 | CA |
| 4 | 246 | 0.57 | 0.79 | 35 | empty |
| 5 | 363 | 0.56 | 0.74 | 43 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1062 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1050 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 398 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5MFO · Designed armadillo repeat protein YIIIM3AIII · 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 5MFO · PDBe 5MFO
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