Research workbench
In silico and in vitro co-evolution of a high affinity complementary protein-protein interface
Analyse In silico and in vitro co-evolution of a high affinity complementary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q9U
- Type
- protein
- Length
- 589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CoA binding protein; Consensus ankyrin repeat
- Ligands
- COA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CoA binding protein | protein | 138 | 32% helix, 20% strand | — |
| B | CoA binding protein | protein | 136 | 29% helix, 20% strand | — |
| C | Consensus ankyrin repeat | protein | 157 | 54% helix, 0% strand | — |
| D | Consensus ankyrin repeat | protein | 158 | 53% helix, 0% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.72 | 0.77 | 88 | COA |
| 2 | 708 | 0.70 | 0.77 | 58 | COA |
| 3 | 165 | 0.45 | 0.76 | 21 | empty |
| 4 | 120 | 0.40 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 839 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 683 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3Q9U · In silico and in vitro co-evolution of a high affinity complementary protein-protein… · 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 3Q9U · PDBe 3Q9U
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