MolNFT v1 · #110997 · protein
Crystal structure of broadly and potently neutralizing antibody 44- VRC13.01 in complex with HIV-1 clade ae strain 93TH057 GP120
4YDJ · Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160: “Crystal structure of broadly and potently neutralizing antibody 44- VRC13.01 in complex with HIV-1 clade ae…”. X-ray diffraction, 3 ligands (NAG, NA, CL), 20 pockets (best…
- PDB
- 4YDJ
- Type
- protein
- Length
- 1,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160; Heavy chain of antibody…
- UniProt
- Q0ED31
- Ligands
- NAG, NA, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 298 | 19% helix, 36% strand | Q0ED31 |
| H, A | Heavy chain of antibody 44-VRC13.01 | protein | 238 | 5% helix, 48% strand | — |
| L, B | Light chain of antibody 44-VRC13.01 | protein | 205 | 7% helix, 46% strand | — |
| I | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 292 | 18% helix, 36% strand | Q0ED31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains G, H, L, I, A, B
- NA · Sodium ion · metal · chains H, L
- CL · Chloride ion · ion · chains B
- BU3 · (R,R)-2,3-butanediol · additive · 4 copies · chains H, A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains H, L, A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.80 | 0.81 | 102 | NAG |
| 2 | 712 | 0.67 | 0.75 | 68 | BU3 |
| 3 | 608 | 0.63 | 0.74 | 60 | empty |
| 4 | 342 | 0.62 | 0.79 | 31 | empty |
| 5 | 377 | 0.62 | 0.78 | 42 | NAG |
Interfaces
10 interfaces between chains.
- H–L · 2095 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1969 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 956 Ų buried · 20 hydrogen bonds · protein-protein
- I–A · 921 Ų buried · 24 hydrogen bonds · protein-protein
- G–A · 289 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 23 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 4YDJ · Crystal structure of broadly and potently neutralizing antibody 44-VRC13.01 in complex… · 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 4YDJ · PDBe 4YDJ · UniProt Q0ED31
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