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
- 4M8Q
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GEP1 fv heavy chain; GEP1 fv light chain; 4E10 epitope scaffold T117
- UniProt
- P18136
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GEP1 fv heavy chain | protein | 125 | 2% helix, 56% strand | — |
| B, L | GEP1 fv light chain | protein | 106 | 6% helix, 55% strand | P18136 |
| C | 4E10 epitope scaffold T117 | protein | 148 | 45% helix, 24% strand | — |
| H | GEP1 fv heavy chain | protein | 125 | 2% helix, 55% strand | — |
| S | 4E10 epitope scaffold T117 | protein | 154 | 43% helix, 23% strand | — |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.56 | 0.87 | 32 | empty |
| 2 | 85 | 0.48 | 0.81 | 23 | empty |
| 3 | 152 | 0.44 | 0.75 | 28 | empty |
| 4 | 124 | 0.43 | 0.76 | 18 | empty |
| 5 | 107 | 0.42 | 0.77 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–S · 786 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 720 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 717 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 703 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 308 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4M8Q · Ontogeny of recognition specificity and functionality for the anti-HIV neutralizing… · 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
- Every structure of UniProt P18136
- Elsewhere: RCSB PDB 4M8Q · PDBe 4M8Q · UniProt P18136
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