MolNFT v1 · #126857 · protein
Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)5
5MFH: “Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)5”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.81). MolNFT v1 #126857 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFH
- Type
- protein
- Length
- 1,145 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM5AII; (RR)5
- Ligands
- CA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YIIIM5AII | protein | 283 | 80% helix, 0% strand | — |
| B | YIIIM5AII | protein | 283 | 77% helix, 0% strand | — |
| C | YIIIM5AII | protein | 281 | 79% helix, 0% strand | — |
| D | YIIIM5AII | protein | 282 | 77% helix, 0% strand | — |
| E, F | (RR)5 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 21 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.81 | 0.86 | 77 | empty |
| 2 | 368 | 0.74 | 0.85 | 43 | empty |
| 3 | 875 | 0.74 | 0.78 | 59 | empty |
| 4 | 449 | 0.70 | 0.81 | 43 | empty |
| 5 | 480 | 0.67 | 0.79 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1544 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1489 Ų buried · 44 hydrogen bonds · protein-protein
- C–F · 901 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 765 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5MFH · 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 5MFH · PDBe 5MFH
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