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Crystal structure of broad and potently neutralizing VRC01-class antibody Z258-VRC27.01, isolated from human donor Z258, in complex with HIV-1 GP120 from clade a strain Q23.17
Analyse Crystal structure of broad and potently neutralizing VRC01-class antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YDI
- Type
- protein
- Length
- 760 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Heavy chain of antibody Z258-VRC27.01; Light chain of…
- UniProt
- O55774
- Ligands
- NAG, SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 343 | 17% helix, 36% strand | O55774 |
| H | Heavy chain of antibody Z258-VRC27.01 | protein | 209 | 9% helix, 50% strand | — |
| L | Light chain of antibody Z258-VRC27.01 | protein | 208 | 4% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains G, L
- SO4 · Sulfate ion · ion · 4 copies · chains G, H
- EDO · 1,2-ethanediol · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.77 | 0.88 | 51 | SO4 |
| 2 | 54 | 0.70 | 0.97 | 19 | empty |
| 3 | 534 | 0.65 | 0.77 | 54 | empty |
| 4 | 242 | 0.56 | 0.78 | 38 | empty |
| 5 | 138 | 0.51 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1610 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1044 Ų buried · 19 hydrogen bonds · protein-protein
- G–L · 217 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 11 disulfide (N-glycosylation, disulfide).
Compared structures
- 4YDI · Crystal structure of broad and potently neutralizing VRC01-class antibody Z258-VRC27.01… · 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 O55774
- Elsewhere: RCSB PDB 4YDI · PDBe 4YDI · UniProt O55774
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