Research workbench
Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 GP120
Analyse Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YFL
- Type
- protein
- Length
- 1,547 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160, envelope glycoprotein GP160…
- UniProt
- Q0ED31
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, E | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160, envelope glycoprotein GP160 | protein | 347 | 18% helix, 36% strand | Q0ED31 |
| H | 1B2530 heavy chain | protein | 223 | 6% helix, 35% strand | — |
| L | 1B2530 light chain | protein | 209 | 4% helix, 21% strand | — |
| F | 1B2530 heavy chain | protein | 221 | 1% helix, 39% strand | — |
| I | 1B2530 light chain | protein | 200 | 4% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains G, E, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.90 | 0.92 | 169 | empty |
| 2 | 349 | 0.80 | 0.90 | 54 | NAG |
| 3 | 352 | 0.79 | 0.88 | 46 | empty |
| 4 | 653 | 0.75 | 0.81 | 78 | empty |
| 5 | 227 | 0.71 | 0.87 | 41 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1739 Ų buried · 6 hydrogen bonds · protein-protein
- F–I · 1539 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 899 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 841 Ų buried · 11 hydrogen bonds · protein-protein
- G–E · 508 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4YFL · Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in… · the same entry in another collection · chain G against G, 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 Q0ED31
- Elsewhere: RCSB PDB 4YFL · PDBe 4YFL · UniProt Q0ED31
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