MolNFT v1 · #116423 · protein
Crystal structures in an anti-HIV antibody lineage from immunization of rhesus macaques
5DD6 · Anti-HIV antibody DH570.MUT58 Fab heavy chain: “Crystal structures in an anti-HIV antibody lineage from immunization of rhesus macaques”. X-ray diffraction, 7 pockets (best druggability 0.68). MolNFT v1 #116423 on GenesisL1: 3D…
- PDB
- 5DD6
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HIV antibody DH570.MUT58 Fab heavy chain; Anti-HIV antibody DH570.MUT58 Fab light…
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-HIV antibody DH570.MUT58 Fab heavy chain | protein | 219 | 8% helix, 55% strand | — |
| L, B | Anti-HIV antibody DH570.MUT58 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| A | Anti-HIV antibody DH570.MUT58 Fab heavy chain | protein | 213 | 6% helix, 54% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.68 | 0.74 | 104 | empty |
| 2 | 263 | 0.48 | 0.73 | 34 | empty |
| 3 | 244 | 0.47 | 0.73 | 42 | empty |
| 4 | 69 | 0.46 | 0.83 | 20 | empty |
| 5 | 119 | 0.42 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1882 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1769 Ų buried · 7 hydrogen bonds · protein-protein
- H–B · 98 Ų buried · 1 hydrogen bond · protein-protein
- L–B · 97 Ų buried · 1 hydrogen bond · protein-protein
- L–A · 56 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5DD6 · Crystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques · 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 5DD6 · PDBe 5DD6
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