Research workbench
Crystal structure of human anti-HIV-1 GP120-reactive antibody 47E Fab
Analyse Crystal structure of human anti-HIV-1 GP120-reactive antibody 47E Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RZI
- Type
- protein
- Length
- 3,417 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 47E light chain; Fab 47E heavy chain
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, I, K, M, O | Fab 47E light chain | protein | 211 | 2% helix, 47% strand | — |
| B, D, H, J, N, P | Fab 47E heavy chain | protein | 216 | 7% helix, 42% strand | — |
| C | Fab 47E light chain | protein | 212 | 5% helix, 46% strand | — |
| F | Fab 47E heavy chain | protein | 217 | 4% helix, 33% strand | — |
| L | Fab 47E heavy chain | protein | 215 | 7% helix, 43% strand | — |
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 | 1045 | 0.78 | 0.80 | 148 | empty |
| 2 | 745 | 0.77 | 0.81 | 76 | empty |
| 3 | 945 | 0.76 | 0.79 | 97 | empty |
| 4 | 1114 | 0.76 | 0.78 | 130 | empty |
| 5 | 508 | 0.74 | 0.83 | 72 | empty |
Interfaces
35 interfaces between chains.
- O–P · 1783 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1757 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1738 Ų buried · 10 hydrogen bonds · protein-protein
- M–N · 1728 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1720 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 1RZI · Crystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab · 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 1RZI · PDBe 1RZI
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