Research workbench
Crystal structure of short afifavidin - biotin complex
Analyse Crystal structure of short afifavidin - biotin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDT
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short afifavidin
- Ligands
- BTN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short afifavidin | protein | 127 | 6% helix, 58% strand | — |
| B | Short afifavidin | protein | 124 | 6% helix, 63% strand | — |
| C | Short afifavidin | protein | 125 | 6% helix, 62% strand | — |
| D | Short afifavidin | protein | 116 | 0% helix, 67% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.73 | 0.81 | 63 | BTN |
| 2 | 502 | 0.72 | 0.81 | 53 | BTN |
| 3 | 288 | 0.56 | 0.77 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1437 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 1394 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6HDT · crystal structure of short afifavidin - biotin complex · 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 6HDT · PDBe 6HDT
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