MolNFT v1 · #166577 · protein
Crystal structure of broad and potent HIV-1 neutralizing antibody 438- D5
6UUL · D5 Fab heavy chain: “Crystal structure of broad and potent HIV-1 neutralizing antibody 438- D5”. X-ray diffraction, 2 ligands (NAG, FUC), 7 pockets (best druggability 0.70). MolNFT v1 #166577 on GenesisL1: 3D structure, binding…
- PDB
- 6UUL
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D5 Fab heavy chain; D5 Fab light chain
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D5 Fab heavy chain | protein | 230 | 7% helix, 48% strand | — |
| B, D | D5 Fab light chain | protein | 215 | 7% helix, 54% strand | — |
| C | D5 Fab heavy chain | protein | 215 | 8% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · chains B
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.70 | 0.74 | 125 | empty |
| 2 | 483 | 0.66 | 0.78 | 57 | empty |
| 3 | 571 | 0.62 | 0.74 | 50 | empty |
| 4 | 174 | 0.50 | 0.77 | 27 | empty |
| 5 | 186 | 0.47 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1819 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1703 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 374 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6UUL · Crystal structure of broad and potent HIV-1 neutralizing antibody 438-D5 · 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 6UUL · PDBe 6UUL
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