MolNFT v1 · #158713 · protein
Crystal structure of 4493 Fab in complex with circumsporozoite protein npdp and anti-kappa vhh domain
6O29 · 4493 Fab heavy chain: “Crystal structure of 4493 Fab in complex with circumsporozoite protein npdp and anti-kappa vhh domain”. X-ray diffraction, 15 pockets (best druggability 0.68). MolNFT v1 #158713 on GenesisL1: 3D structure…
- PDB
- 6O29
- Type
- protein
- Length
- 1,140 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4493 Fab heavy chain; 4493 kappa light chain; Circumsporozoite protein; Anti-kappa vhh…
- UniProt
- P02893
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4493 Fab heavy chain | protein | 217 | 7% helix, 52% strand | — |
| B, L | 4493 kappa light chain | protein | 214 | 7% helix, 50% strand | — |
| H | 4493 Fab heavy chain | protein | 223 | 9% helix, 51% strand | — |
| C | Circumsporozoite protein | protein | 15 | 0% helix, 0% strand | P02893 |
| D | Circumsporozoite protein | protein | 15 | 0% helix, 0% strand | P02893 |
| K, E | Anti-kappa vhh domain | protein | 121 | 7% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.68 | 0.95 | 27 | empty |
| 2 | 560 | 0.67 | 0.77 | 83 | empty |
| 3 | 97 | 0.65 | 0.91 | 32 | empty |
| 4 | 485 | 0.63 | 0.76 | 68 | empty |
| 5 | 126 | 0.58 | 0.84 | 29 | empty |
Interfaces
14 interfaces between chains.
- H–L · 1943 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1738 Ų buried · 15 hydrogen bonds · protein-protein
- L–E · 610 Ų buried · 7 hydrogen bonds · protein-protein
- B–K · 605 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6O29 · Crystal structure of 4493 Fab in complex with circumsporozoite protein NPDP and… · the same entry in another collection · chain E against E, TM-score 1.00
- P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain C against A, TM-score 0.30
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 6O29 · PDBe 6O29 · UniProt P02893
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