Research workbench
Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with mn peptide
Analyse Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with mn peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B0S
- Type
- protein
- Length
- 457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2219, light chain; Fab 2219, heavy chain; Mn peptide of exterior membrane…
- UniProt
- P05877
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 2219, light chain | protein | 215 | 7% helix, 50% strand | — |
| H | Fab 2219, heavy chain | protein | 226 | 7% helix, 51% strand | — |
| P | Mn peptide of exterior membrane glycoprotein GP120 | protein | 16 | 0% helix, 50% strand | P05877 |
Ligands and binding sites
- ACY · Acetic acid · additive · 3 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.62 | 0.74 | 72 | EDO |
| 2 | 93 | 0.36 | 0.75 | 22 | empty |
| 3 | 80 | 0.31 | 0.73 | 17 | empty |
| 4 | 68 | 0.30 | 0.74 | 15 | empty |
| 5 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1764 Ų buried · 24 hydrogen bonds · protein-protein
- H–P · 621 Ų buried · 16 hydrogen bonds · protein-protein
- L–P · 379 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2B0S · Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with MN peptide · 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 P05877
- Elsewhere: RCSB PDB 2B0S · PDBe 2B0S · UniProt P05877
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