Research workbench
Structure of the anti-HIV antibody DH501 that binds GP120 V3 glycan and the base of V3 with free MAN9 glycan
Analyse Structure of the anti-HIV antibody DH501 that binds GP120 V3 glycan and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T4Z
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody DH501 Fab heavy chain; Antibody DH501 Fab light chain
- Ligands
- MAN, CA
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody DH501 Fab heavy chain | protein | 227 | 7% helix, 50% strand | — |
| L | Antibody DH501 Fab light chain | protein | 213 | 8% helix, 50% strand | — |
| A | Antibody DH501 Fab heavy chain | protein | 218 | 7% helix, 52% strand | — |
| B | Antibody DH501 Fab light chain | protein | 210 | 9% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains H
- CA · Calcium ion · metal · 2 copies · chains H, L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.62 | 0.75 | 55 | empty |
| 2 | 315 | 0.58 | 0.77 | 47 | empty |
| 3 | 367 | 0.56 | 0.75 | 50 | CA |
| 4 | 403 | 0.55 | 0.74 | 47 | empty |
| 5 | 94 | 0.47 | 0.81 | 29 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1981 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1884 Ų buried · 11 hydrogen bonds · protein-protein
- L–B · 304 Ų buried · 7 hydrogen bonds · protein-protein
- H–B · 164 Ų buried · 1 hydrogen bond · protein-protein
- L–A · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5T4Z · Structure of the anti-HIV antibody DH501 that binds GP120 V3 glycan and the base of V3… · the same entry in another collection · chain H against H, 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 5T4Z · PDBe 5T4Z
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