Research workbench
Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alpharep)
Analyse Selection of specific protein binders for pre-defined targets from an optimized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JW3
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neocarzinostatin; Alpha-helical artificial proteins
- UniProt
- P0A3S0
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neocarzinostatin | protein | 111 | 0% helix, 56% strand | P0A3S0 |
| B | Neocarzinostatin | protein | 112 | 0% helix, 58% strand | P0A3S0 |
| C | Alpha-helical artificial proteins | protein | 97 | 72% helix, 0% strand | — |
| D | Alpha-helical artificial proteins | protein | 96 | 70% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.71 | 0.85 | 37 | empty |
| 2 | 74 | 0.35 | 0.76 | 15 | empty |
| 3 | 52 | 0.26 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 780 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 772 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 649 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 266 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 259 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4JW3 · Selection of specific protein binders for pre-defined targets from an optimized library… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3S0 · AlphaFold monomer V2.0 prediction for neocarzinostatin (P0A3S0) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A3S0
- Elsewhere: RCSB PDB 4JW3 · PDBe 4JW3 · UniProt P0A3S0
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