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Crystal structure of HIV-GP120 core in complex with CD4-binding site antibody B13, space group C222
Analyse Crystal structure of HIV-GP120 core in complex with CD4-binding site antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IDX
- Type
- protein
- Length
- 749 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 HXBC2 GP120 core; Fab B13 heavy chain; Fab B13 light chain
- Ligands
- NAG, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 HXBC2 GP120 core | protein | 306 | 15% helix, 41% strand | — |
| H | Fab B13 heavy chain | protein | 229 | 7% helix, 48% strand | — |
| L | Fab B13 light chain | protein | 214 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains G, H
- SO4 · Sulfate ion · ion · 4 copies · chains G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains G, H
- GOL · Glycerol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.74 | 0.82 | 73 | EPE, SO4 |
| 2 | 661 | 0.65 | 0.75 | 62 | empty |
| 3 | 112 | 0.58 | 0.85 | 22 | NAG |
| 4 | 302 | 0.56 | 0.76 | 38 | empty |
| 5 | 150 | 0.51 | 0.79 | 27 | NAG, SO4 |
Interfaces
2 interfaces between chains.
- H–L · 2032 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 756 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 3IDX · Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space… · 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
- Elsewhere: RCSB PDB 3IDX · PDBe 3IDX
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