Research workbench
Designed armadillo repeat protein (KR)5_GS10_YIIIM6AII
Analyse Designed armadillo repeat protein (KR)5_GS10_YIIIM6AII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MFL
- Type
- protein
- Length
- 999 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (KR)5_GS10_YIIIM6AII
- Ligands
- CA, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (KR)5_GS10_YIIIM6AII | protein | 332 | 76% helix, 0% strand | — |
| B | (KR)5_GS10_YIIIM6AII | protein | 333 | 76% helix, 0% strand | — |
| C | (KR)5_GS10_YIIIM6AII | protein | 334 | 75% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.77 | 0.79 | 83 | MPD |
| 2 | 904 | 0.77 | 0.80 | 93 | CA, EDO, MG |
| 3 | 84 | 0.59 | 0.88 | 18 | MPD |
| 4 | 110 | 0.39 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1644 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5MFL · Designed armadillo repeat protein (KR)5_GS10_YIIIM6AII · 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 5MFL · PDBe 5MFL
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