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Crystal structure of broadly neutralizing antibody CH03, isolated from donor CH0219, in complex with scaffolded trimeric HIV-1 env V1V2 domain from the clade C superinfecting strain of donor CAP256.
Analyse Crystal structure of broadly neutralizing antibody CH03, 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
- 5ESV
- Type
- protein
- Length
- 1,872 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH03 heavy chain; CH03 light chain; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate…
- EC
- 4.6.1.12
- UniProt
- S6BGE0, P01834, P44815, W6ICC0
- Ligands
- MAN, NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | CH03 heavy chain | protein | 230 | 7% helix, 50% strand | S6BGE0 |
| B | CH03 light chain | protein | 213 | 7% helix, 55% strand | P01834 |
| D, L | CH03 light chain | protein | 214 | 6% helix, 50% strand | P01834 |
| E | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, envelope glycoprotein GP160 (EC 4.6.1.12) | protein | 176 | 23% helix, 39% strand | P44815, W6ICC0 |
| F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, envelope glycoprotein GP160 (EC 4.6.1.12) | protein | 179 | 25% helix, 38% strand | P44815, W6ICC0 |
| G | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, envelope glycoprotein GP160 (EC 4.6.1.12) | protein | 187 | 25% helix, 34% strand | P44815, W6ICC0 |
| H | CH03 heavy chain | protein | 229 | 4% helix, 48% strand | S6BGE0 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 28 copies · chains A, L, H, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, E, G, H, L, C, F, B, D
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains A, H, L, C, B, D
- ZN · Zinc ion · metal · 3 copies · chains E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.75 | 0.78 | 111 | ZN |
| 2 | 687 | 0.75 | 0.81 | 102 | empty |
| 3 | 836 | 0.68 | 0.75 | 87 | empty |
| 4 | 613 | 0.65 | 0.75 | 69 | empty |
| 5 | 631 | 0.65 | 0.75 | 67 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1913 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1750 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 1419 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1079 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5ESV · Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in… · the same entry in another collection · chain L against L, 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 F against A, TM-score 0.65
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 S6BGE0
- Every structure of UniProt P01834
- Every structure of UniProt P44815
- Every structure of UniProt W6ICC0
- Elsewhere: RCSB PDB 5ESV · PDBe 5ESV · UniProt S6BGE0 · UniProt P01834 · UniProt P44815 · UniProt W6ICC0
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