MolNFT v1 · #108332 · protein
Designed armadillo repeat protein with 4 internal repeats, 2ND generation C-cap and 3RD generation N-cap.
4V3Q · YIII_M4_AII: “Designed armadillo repeat protein with 4 internal repeats, 2ND generation C-cap and 3RD generation N-cap.”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.77). MolNFT v1 #108332 on GenesisL1: 3D…
- PDB
- 4V3Q
- Type
- protein
- Length
- 983 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIII_M4_AII
- Ligands
- CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | YIII_M4_AII | protein | 247 | 72% helix, 0% strand | — |
| C | YIII_M4_AII | protein | 245 | 72% helix, 0% strand | — |
| D | YIII_M4_AII | protein | 244 | 73% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.77 | 0.86 | 61 | empty |
| 2 | 394 | 0.76 | 0.86 | 51 | GOL |
| 3 | 195 | 0.69 | 0.87 | 38 | empty |
| 4 | 146 | 0.63 | 0.86 | 31 | empty |
| 5 | 176 | 0.54 | 0.80 | 36 | CA |
Interfaces
6 interfaces between chains.
- C–D · 1266 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1113 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1107 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 181 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4V3Q · Designed armadillo repeat protein with 4 internal repeats, 2nd generation C-cap and 3rd… · 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 4V3Q · PDBe 4V3Q
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