MolNFT v1 · #104302 · protein
Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1- neutralizing antibody in complex with CD4
4Q6I · Light chain of murine 2D5 Fab: “Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1- neutralizing antibody in complex with CD4”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #104302 on GenesisL1: 3D…
- PDB
- 4Q6I
- Type
- protein
- Length
- 2,488 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of murine 2D5 Fab; Heavy chain of murine 2D5 Fab; T-cell surface glycoprotein…
- UniProt
- P01730
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, L | Light chain of murine 2D5 Fab | protein | 218 | 6% helix, 52% strand | — |
| B, E, G, H | Heavy chain of murine 2D5 Fab | protein | 222 | 4% helix, 49% strand | — |
| C, I, J, K | T-cell surface glycoprotein CD4 | protein | 182 | 5% helix, 52% strand | P01730 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.79 | 0.85 | 56 | empty |
| 2 | 563 | 0.77 | 0.84 | 62 | empty |
| 3 | 448 | 0.65 | 0.78 | 46 | empty |
| 4 | 218 | 0.64 | 0.83 | 35 | empty |
| 5 | 200 | 0.62 | 0.83 | 34 | empty |
Interfaces
21 interfaces between chains.
- D–E · 2027 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2019 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1980 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1952 Ų buried · 14 hydrogen bonds · protein-protein
- B–K · 512 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide (disulfide).
Compared structures
- 4Q6I · Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 4Q6I · PDBe 4Q6I · UniProt P01730
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.