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Crystal structure of broadly neutralizing antibody CH04, isolated from donor CH0219, in complex with scaffolded trimeric HIV-1 env V1V2 domain from the clade ae strain A244
Analyse Crystal structure of broadly neutralizing antibody CH04, isolated from donor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ESZ
- Type
- protein
- Length
- 1,171 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH04 heavy chain; CH04 light chain; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate…
- EC
- 4.6.1.12
- UniProt
- A0A087WYE1, P01834, P44815, Q4QX31
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CH04 heavy chain | protein | 229 | 8% helix, 49% strand | A0A087WYE1 |
| L | CH04 light chain | protein | 214 | 7% helix, 53% strand | P01834 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, envelope glycoprotein GP160 (EC 4.6.1.12) | protein | 163 | 28% helix, 29% strand | P44815, Q4QX31 |
| G | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, envelope glycoprotein GP160 (EC 4.6.1.12) | protein | 142 | 31% helix, 31% strand | P44815, Q4QX31 |
| A | CH04 heavy chain | protein | 212 | 8% helix, 42% strand | A0A087WYE1 |
| B | CH04 light chain | protein | 211 | 8% helix, 48% strand | P01834 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains H, L, C, A, G, B
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains H, L, A, B, G
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.73 | 0.78 | 77 | empty |
| 2 | 668 | 0.65 | 0.75 | 71 | empty |
| 3 | 63 | 0.54 | 0.88 | 21 | empty |
| 4 | 352 | 0.54 | 0.74 | 40 | empty |
| 5 | 156 | 0.47 | 0.77 | 26 | NAG |
Interfaces
7 interfaces between chains.
- H–L · 1906 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1583 Ų buried · 6 hydrogen bonds · protein-protein
- H–G · 424 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 258 Ų buried · 0 hydrogen bonds · protein-protein
- H–A · 208 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5ESZ · Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in… · the same entry in another collection · chain B against B, TM-score 1.00
- P44815 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain C against A, TM-score 0.69
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 A0A087WYE1
- Every structure of UniProt P01834
- Every structure of UniProt P44815
- Every structure of UniProt Q4QX31
- Elsewhere: RCSB PDB 5ESZ · PDBe 5ESZ · UniProt A0A087WYE1 · UniProt P01834 · UniProt P44815 · UniProt Q4QX31
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