MolNFT v1 · #158715 · protein
Crystal structure of 4493 Fab in complex with circumsporozoite protein dnd and anti-kappa vhh domain
6O2B · 4493 Fab heavy chain: “Crystal structure of 4493 Fab in complex with circumsporozoite protein dnd and anti-kappa vhh domain”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #158715 on GenesisL1: 3D structure…
- PDB
- 6O2B
- Type
- protein
- Length
- 2,257 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4493 Fab heavy chain; 4493 kappa light chain; Anti-kappa vhh domain; Circumsporozoite…
- UniProt
- P02893
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 9 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4493 Fab heavy chain | protein | 217 | 8% helix, 50% strand | — |
| B, D, I, P | 4493 kappa light chain | protein | 214 | 7% helix, 54% strand | — |
| C | 4493 Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| H, O | 4493 Fab heavy chain | protein | 218 | 8% helix, 51% strand | — |
| E | Anti-kappa vhh domain | protein | 120 | 5% helix, 49% strand | — |
| J | Anti-kappa vhh domain | protein | 119 | 5% helix, 51% strand | — |
| M | Anti-kappa vhh domain | protein | 121 | 5% helix, 49% strand | — |
| F, G, K, L | Circumsporozoite protein | protein | 12 | 25% helix, 0% strand | P02893 |
| N | Anti-kappa vhh domain | protein | 120 | 5% helix, 49% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 8 copies · chains A, C, G, H, O, P
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.70 | 0.79 | 72 | empty |
| 2 | 725 | 0.70 | 0.77 | 70 | empty |
| 3 | 76 | 0.69 | 0.95 | 29 | empty |
| 4 | 73 | 0.69 | 0.95 | 30 | empty |
| 5 | 768 | 0.68 | 0.75 | 87 | ACT |
Interfaces
36 interfaces between chains.
- A–B · 1807 Ų buried · 18 hydrogen bonds · protein-protein
- O–P · 1803 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1796 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1759 Ų buried · 14 hydrogen bonds · protein-protein
- B–N · 625 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6O2B · Crystal structure of 4493 Fab in complex with circumsporozoite protein DND and anti-kappa… · the same entry in another collection · chain N against N, 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 P02893
- Elsewhere: RCSB PDB 6O2B · PDBe 6O2B · UniProt P02893
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