Research workbench
Ontogeny of recognition specificity and functionality for the anti-HIV neutralizing antibody 4E10
Analyse Ontogeny of recognition specificity and functionality for the anti-HIV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M62
- Type
- protein
- Length
- 789 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GEP2 fv light chain; GEP2 fv heavy chain; T117
- UniProt
- P18136
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | GEP2 fv light chain | protein | 113 | 5% helix, 53% strand | P18136 |
| H | GEP2 fv heavy chain | protein | 127 | 7% helix, 52% strand | — |
| I | GEP2 fv heavy chain | protein | 126 | 5% helix, 52% strand | — |
| S, T | T117 | protein | 155 | 41% helix, 23% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains L, M, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.79 | 0.81 | 102 | empty |
| 2 | 75 | 0.42 | 0.80 | 24 | empty |
| 3 | 77 | 0.41 | 0.79 | 20 | empty |
| 4 | 83 | 0.39 | 0.77 | 23 | empty |
| 5 | 86 | 0.37 | 0.76 | 19 | empty |
Interfaces
9 interfaces between chains.
- I–T · 926 Ų buried · 8 hydrogen bonds · protein-protein
- H–S · 843 Ų buried · 9 hydrogen bonds · protein-protein
- M–I · 685 Ų buried · 5 hydrogen bonds · protein-protein
- L–H · 680 Ų buried · 5 hydrogen bonds · protein-protein
- H–I · 287 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4M62 · Ontogeny of recognition specificity and functionality for the anti-HIV neutralizing… · 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 P18136
- Elsewhere: RCSB PDB 4M62 · PDBe 4M62 · UniProt P18136
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