Research workbench
ZEBAVIDIN
Analyse ZEBAVIDIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJ8
- Type
- protein
- Length
- 1,908 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zebavidin
- UniProt
- E7F650
- Ligands
- BTN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, I, J | Zebavidin | protein | 119 | 3% helix, 54% strand | E7F650 |
| B, F, H, N | Zebavidin | protein | 118 | 0% helix, 53% strand | E7F650 |
| K | Zebavidin | protein | 120 | 4% helix, 53% strand | E7F650 |
| L | Zebavidin | protein | 121 | 7% helix, 53% strand | E7F650 |
| M, P | Zebavidin | protein | 120 | 6% helix, 53% strand | E7F650 |
| O | Zebavidin | protein | 122 | 4% helix, 52% strand | E7F650 |
Ligands and binding sites
- BTN · Biotin · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · chains J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.78 | 0.80 | 89 | empty |
| 2 | 1178 | 0.78 | 0.80 | 119 | BTN |
| 3 | 81 | 0.75 | 0.97 | 19 | BTN |
| 4 | 83 | 0.75 | 0.97 | 18 | BTN |
| 5 | 84 | 0.74 | 0.96 | 20 | BTN |
Interfaces
37 interfaces between chains.
- M–P · 1660 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 1638 Ų buried · 18 hydrogen bonds · protein-protein
- I–L · 1637 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1629 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1624 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4BJ8 · Zebavidin · 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
- Every structure of UniProt E7F650
- Elsewhere: RCSB PDB 4BJ8 · PDBe 4BJ8 · UniProt E7F650
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