MolNFT v1 · #126856 · protein
Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)4
5MFG: “Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)4”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.90). MolNFT v1 #126856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFG
- Type
- protein
- Length
- 1,072 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM5AII; (RR)4
- Ligands
- CA
- Pockets
- 5 · best druggability 0.90
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YIIIM5AII | protein | 282 | 74% helix, 0% strand | — |
| B | YIIIM5AII | protein | 269 | 76% helix, 0% strand | — |
| C | YIIIM5AII | protein | 270 | 73% helix, 0% strand | — |
| D | YIIIM5AII | protein | 241 | 76% helix, 0% strand | — |
| E | (RR)4 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.90 | 0.95 | 85 | empty |
| 2 | 1095 | 0.77 | 0.79 | 100 | CA |
| 3 | 407 | 0.68 | 0.80 | 53 | empty |
| 4 | 52 | 0.67 | 0.97 | 16 | empty |
| 5 | 259 | 0.60 | 0.79 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1626 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1388 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1380 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 901 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 782 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5MFG · Designed armadillo repeat protein YIIIM5AII in complex with peptide (RR)4 · 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 5MFG · PDBe 5MFG
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