MolNFT v1 · #165954 · protein
N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6UBI · VRC34.05 heavy chain: “N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #165954 on GenesisL1: 3D structure, binding sites…
- PDB
- 6UBI
- Type
- protein
- Length
- 875 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC34.05 heavy chain; VRC34.05 light chain; HIV fusion peptide 512-519
- UniProt
- P0DOX5, Q6GMX0
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VRC34.05 heavy chain | protein | 215 | 7% helix, 51% strand | P0DOX5 |
| B, E | VRC34.05 light chain | protein | 212 | 6% helix, 50% strand | Q6GMX0 |
| C, F | HIV fusion peptide 512-519 | protein | 8 | 0% helix, 0% strand | — |
| D | VRC34.05 heavy chain | protein | 220 | 7% helix, 50% strand | P0DOX5 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.73 | 0.76 | 98 | empty |
| 2 | 630 | 0.64 | 0.75 | 59 | empty |
| 3 | 425 | 0.58 | 0.75 | 55 | empty |
| 4 | 457 | 0.58 | 0.74 | 55 | empty |
| 5 | 52 | 0.46 | 0.85 | 23 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1749 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1738 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 465 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 249 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6UBI · N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519 · the same entry in another collection · chain A against A, 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 P0DOX5
- Every structure of UniProt Q6GMX0
- Elsewhere: RCSB PDB 6UBI · PDBe 6UBI · UniProt P0DOX5 · UniProt Q6GMX0
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