MolNFT v1 · #67208 · protein
Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 Fab' fragment in complex with GP41 peptide analog ELD(ORN)WAS
3IDJ · 2F5 Fab light chain: “Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 Fab' fragment in complex with GP41…”. X-ray diffraction, 2 pockets (best druggability 0.59). MolNFT v1 #67208 on GenesisL1: 3D…
- PDB
- 3IDJ
- Type
- protein
- Length
- 450 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F5 Fab light chain; 2F5 Fab heavy chain; GP41 mper peptide analog
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2F5 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| B | 2F5 Fab heavy chain | protein | 229 | 8% helix, 52% strand | — |
| C | GP41 mper peptide analog | protein | 7 | 0% helix, 14% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.59 | 0.75 | 45 | empty |
| 2 | 92 | 0.37 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1857 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 351 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 3IDJ · Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment… · 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 3IDJ · PDBe 3IDJ
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