MolNFT v1 · #167566 · protein
Crystal structure of macaque anti-HIV-1 antibody RM20E1
6VOR · RM20E1 Fab heavy chain: “Crystal structure of macaque anti-HIV-1 antibody RM20E1”. X-ray diffraction, 1 ligand (GLY), 10 pockets (best druggability 0.60). MolNFT v1 #167566 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VOR
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RM20E1 Fab heavy chain; RM20E1 Fab light chain
- Ligands
- GLY
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RM20E1 Fab heavy chain | protein | 218 | 7% helix, 54% strand | — |
| B | RM20E1 Fab light chain | protein | 218 | 6% helix, 50% strand | — |
| C | RM20E1 Fab heavy chain | protein | 218 | 7% helix, 55% strand | — |
| D | RM20E1 Fab light chain | protein | 217 | 6% helix, 50% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
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 | 325 | 0.60 | 0.78 | 46 | empty |
| 2 | 553 | 0.59 | 0.73 | 74 | GLY |
| 3 | 356 | 0.57 | 0.76 | 47 | empty |
| 4 | 83 | 0.54 | 0.85 | 22 | empty |
| 5 | 319 | 0.53 | 0.74 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1786 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1722 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 494 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 366 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6VOR · Crystal structure of macaque anti-HIV-1 antibody RM20E1 · 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
- Elsewhere: RCSB PDB 6VOR · PDBe 6VOR
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