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Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan and the base of V3
Analyse Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IIE
- Type
- protein
- Length
- 814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- antibody DH501 FabH chain; antibody DH501 light chain
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.8 · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | antibody DH501 FabH chain | protein | 219 | 7% helix, 52% strand | — |
| L | antibody DH501 light chain | protein | 211 | 9% helix, 51% strand | — |
| A | antibody DH501 FabH chain | protein | 210 | 9% helix, 50% strand | — |
| B | antibody DH501 light chain | protein | 174 | 5% helix, 45% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.70 | 0.78 | 55 | empty |
| 2 | 312 | 0.51 | 0.73 | 39 | empty |
| 3 | 158 | 0.41 | 0.74 | 23 | empty |
| 4 | 78 | 0.41 | 0.79 | 27 | empty |
| 5 | 79 | 0.36 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1814 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1777 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 971 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5IIE · Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan and the… · 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 5IIE · PDBe 5IIE
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