MolNFT v1 · #110103 · protein
Crystal structure of Fab of HIV-1 GP120 V3-specific human monoclonal antibody 2424 in complex with jr-fl V3 peptide
4XMK · Light chain of HIV-1 GP120 V3-specific human monoclonal…: “Crystal structure of Fab of HIV-1 GP120 V3-specific human monoclonal antibody 2424 in complex with jr-fl V3…”. X-ray diffraction, 8 pockets (best druggability 0.63). MolNFT…
- PDB
- 4XMK
- Type
- protein
- Length
- 1,326 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of HIV-1 GP120 V3-specific human monoclonal antibody 2424; Heavy chain of…
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Light chain of HIV-1 GP120 V3-specific human monoclonal antibody 2424 | protein | 215 | 6% helix, 51% strand | — |
| H, I | Heavy chain of HIV-1 GP120 V3-specific human monoclonal antibody 2424 | protein | 217 | 4% helix, 55% strand | — |
| P, Q, R | HIV-1 jr-fl GP120 V3 peptide | protein | 11 | 27% helix, 18% strand | — |
| N | Light chain of HIV-1 GP120 V3-specific human monoclonal antibody 2424 | protein | 213 | 6% helix, 51% strand | — |
| J | Heavy chain of HIV-1 GP120 V3-specific human monoclonal antibody 2424 | protein | 216 | 4% helix, 56% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.63 | 0.76 | 67 | empty |
| 2 | 611 | 0.62 | 0.74 | 64 | empty |
| 3 | 572 | 0.61 | 0.74 | 57 | empty |
| 4 | 334 | 0.59 | 0.77 | 39 | empty |
| 5 | 92 | 0.36 | 0.76 | 19 | empty |
Interfaces
12 interfaces between chains.
- N–J · 1774 Ų buried · 21 hydrogen bonds · protein-protein
- L–H · 1726 Ų buried · 18 hydrogen bonds · protein-protein
- M–I · 1706 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 709 Ų buried · 17 hydrogen bonds · protein-protein
- I–N · 524 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4XMK · Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424 in… · the same entry in another collection · chain H against H, 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 4XMK · PDBe 4XMK
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