MolNFT v1 · #114320 · protein
Crystal structure of the neutralizing anti-circumsporozoite protein 580 antibody
5BK3 · 580 antibody, light chain: “Crystal structure of the neutralizing anti-circumsporozoite protein 580 antibody”. X-ray diffraction, 5 ligands (NAG, FUC, MAN), 15 pockets (best druggability 0.79). MolNFT v1 #114320 on GenesisL1: 3D…
- PDB
- 5BK3
- Type
- protein
- Length
- 1,742 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 580 antibody, light chain; 580 antibody, heavy chain
- Ligands
- NAG, FUC, MAN, BMA, SO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D, F | 580 antibody, light chain | protein | 217 | 6% helix, 52% strand | — |
| H | 580 antibody, heavy chain | protein | 219 | 8% helix, 48% strand | — |
| A | 580 antibody, heavy chain | protein | 219 | 7% helix, 48% strand | — |
| C, E | 580 antibody, heavy chain | protein | 218 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains L, A, B, D, H, F
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains L, A, B, D, F
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 12 copies · chains L, H, B, F, A, D, C
- GOL · Glycerol · additive · 21 copies · chains L, B, A, H, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.79 | 0.81 | 102 | GOL |
| 2 | 580 | 0.61 | 0.74 | 67 | GOL |
| 3 | 183 | 0.59 | 0.82 | 30 | GOL |
| 4 | 400 | 0.57 | 0.75 | 52 | SO4 |
| 5 | 74 | 0.57 | 0.88 | 21 | empty |
Interfaces
12 interfaces between chains.
- L–H · 1740 Ų buried · 13 hydrogen bonds · protein-protein
- F–E · 1733 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 1685 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1675 Ų buried · 12 hydrogen bonds · protein-protein
- H–C · 739 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5BK3 · Crystal structure of the neutralizing anti-circumsporozoite protein 580 antibody · the same entry in another collection · chain L against L, 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 5BK3 · PDBe 5BK3
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