MolNFT v1 · #158714 · protein
Crystal structure of 4493 Fab in complex with circumsporozoite protein ndn and anti-kappa vhh domain
6O2A · 4493 Fab heavy chain: “Crystal structure of 4493 Fab in complex with circumsporozoite protein ndn and anti-kappa vhh domain”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #158714 on GenesisL1: 3D structure…
- PDB
- 6O2A
- Type
- protein
- Length
- 2,259 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 0.81
Structure
x-ray diffraction · 10 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4493 Fab heavy chain | protein | 225 | 8% helix, 49% strand | — |
| B | 4493 kappa light chain | protein | 215 | 7% helix, 53% strand | — |
| C | 4493 Fab heavy chain | protein | 221 | 8% helix, 49% strand | — |
| D, I, P | 4493 kappa light chain | protein | 214 | 8% helix, 53% strand | — |
| H | 4493 Fab heavy chain | protein | 221 | 8% helix, 49% strand | — |
| O | 4493 Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| E | Anti-kappa vhh domain | protein | 121 | 5% helix, 50% strand | — |
| F, G, K, L | Circumsporozoite protein | protein | 9 | 0% helix, 0% strand | P02893 |
| M | Anti-kappa vhh domain | protein | 120 | 5% helix, 50% strand | — |
| N, J | Anti-kappa vhh domain | protein | 119 | 5% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, E, C, P, D, H, O, F, I, N
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 | 1067 | 0.81 | 0.82 | 148 | empty |
| 2 | 653 | 0.74 | 0.80 | 71 | empty |
| 3 | 729 | 0.72 | 0.78 | 72 | EDO |
| 4 | 82 | 0.69 | 0.94 | 28 | empty |
| 5 | 482 | 0.68 | 0.79 | 59 | empty |
Interfaces
35 interfaces between chains.
- A–B · 1934 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 1879 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1873 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1847 Ų buried · 15 hydrogen bonds · protein-protein
- D–M · 626 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 6O2A · Crystal structure of 4493 Fab in complex with circumsporozoite protein NDN and anti-kappa… · the same entry in another collection · chain J against J, 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 6O2A · PDBe 6O2A · UniProt P02893
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