MolNFT v1 · #105788 · protein
Crystal structure of adcc-potent rhesus macaque antibody JR4 in complex with HIV-1 clade A/E GP120 and M48
4RFN · HIV-1 clade A/E 93TH057 (H375S) GP120: “Crystal structure of adcc-potent rhesus macaque antibody JR4 in complex with HIV-1 clade A/E GP120 and M48”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 16 pockets (best druggability 0.67).…
- PDB
- 4RFN
- Type
- protein
- Length
- 1,580 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade A/E 93TH057 (H375S) GP120; Fab heavy chain of adcc anti-HIV-1 antibody JR4…
- Ligands
- MPT, NAG, NH2
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A | HIV-1 clade A/E 93TH057 (H375S) GP120 | protein | 337 | 17% helix, 34% strand | — |
| H, B | Fab heavy chain of adcc anti-HIV-1 antibody JR4 | protein | 217 | 3% helix, 47% strand | — |
| L, C | Fab light chain of adcc anti-HIV-1 antibody JR4 | protein | 210 | 5% helix, 47% strand | — |
| M, D | T-cell surface glycoprotein CD4 mimetic M48 | protein | 26 | 35% helix, 31% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains G, M, A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains G, A
- NH2 · Amino group · ion · 2 copies · chains M, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.67 | 0.76 | 59 | empty |
| 2 | 614 | 0.64 | 0.75 | 52 | empty |
| 3 | 127 | 0.62 | 0.86 | 27 | empty |
| 4 | 130 | 0.60 | 0.85 | 27 | empty |
| 5 | 82 | 0.59 | 0.88 | 27 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1871 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1852 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1025 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1020 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 661 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 18 glycan, 4 covalent, 2 d-amino (disulfide, N-glycosylation, covalent ligand, D-amino acid).
Compared structures
- 4RFN · Crystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in complex with HIV-1 CLADE… · 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 4RFN · PDBe 4RFN
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