Research workbench
Crystal structure of 3945 Fab in complex with circumsporozoite protein NANP3 and anti-kappa vhh domain
Analyse Crystal structure of 3945 Fab in complex with circumsporozoite protein NANP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O25
- Type
- protein
- Length
- 1,681 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3945 Fab heavy chain; 3945 kappa light chain; Anti-kappa vhh domain; Circumsporozoite…
- UniProt
- P02893
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3945 Fab heavy chain | protein | 220 | 5% helix, 51% strand | — |
| E | 3945 Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| F, J | 3945 kappa light chain | protein | 214 | 7% helix, 51% strand | — |
| B | 3945 kappa light chain | protein | 213 | 7% helix, 51% strand | — |
| I | 3945 Fab heavy chain | protein | 218 | 6% helix, 50% strand | — |
| K, C, G | Anti-kappa vhh domain | protein | 119 | 5% helix, 54% strand | — |
| D | Circumsporozoite protein | protein | 11 | 0% helix, 0% strand | P02893 |
| H | Circumsporozoite protein | protein | 8 | 0% helix, 13% strand | P02893 |
| L | Circumsporozoite protein | protein | 10 | 0% helix, 10% strand | P02893 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.70 | 0.76 | 98 | empty |
| 2 | 723 | 0.68 | 0.76 | 84 | empty |
| 3 | 77 | 0.68 | 0.94 | 30 | empty |
| 4 | 73 | 0.67 | 0.94 | 30 | empty |
| 5 | 525 | 0.64 | 0.76 | 72 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1701 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1700 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1690 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 589 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 583 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6O25 · Crystal structure of 3945 Fab in complex with circumsporozoite protein NANP3 and… · 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
- Every structure of UniProt P02893
- Elsewhere: RCSB PDB 6O25 · PDBe 6O25 · UniProt P02893
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