Research workbench
Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5
Analyse Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D01
- Type
- protein
- Length
- 1,768 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1210 antibody, heavy chain; 1210 antibody, light chain; NANP5
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1210 antibody, heavy chain | protein | 220 | 6% helix, 50% strand | — |
| B, D, F | 1210 antibody, light chain | protein | 212 | 6% helix, 52% strand | — |
| C | 1210 antibody, heavy chain | protein | 220 | 6% helix, 51% strand | — |
| E | 1210 antibody, heavy chain | protein | 222 | 6% helix, 50% strand | — |
| G | 1210 antibody, heavy chain | protein | 219 | 7% helix, 51% strand | — |
| H | 1210 antibody, light chain | protein | 213 | 6% helix, 51% strand | — |
| I, J | NANP5 | protein | 19 | 0% helix, 11% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, B, F, D, C, E, G, H, I, J
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.76 | 0.80 | 85 | EDO, PEG |
| 2 | 524 | 0.74 | 0.82 | 55 | EDO |
| 3 | 599 | 0.63 | 0.75 | 71 | empty |
| 4 | 205 | 0.62 | 0.82 | 28 | EDO |
| 5 | 183 | 0.60 | 0.82 | 25 | EDO |
Interfaces
23 interfaces between chains.
- E–F · 1868 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1843 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1795 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1739 Ų buried · 13 hydrogen bonds · protein-protein
- E–J · 651 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6D01 · Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5 · the same entry in another collection · chain A against A, 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 6D01 · PDBe 6D01
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