Research workbench
Crystal structure of the 580 germline antibody bound to circumsporozoite protein nanp 5-mer
Analyse Crystal structure of the 580 germline antibody bound to circumsporozoite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AZM
- Type
- protein
- Length
- 904 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 580 germline antibody, light chain; 580 germline antibody, heavy chain; Circumsporozoite…
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 580 germline antibody, light chain | protein | 219 | 5% helix, 52% strand | — |
| B, D | 580 germline antibody, heavy chain | protein | 225 | 8% helix, 48% strand | — |
| F, E | Circumsporozoite protein nanp 5-mer | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.66 | 0.75 | 76 | empty |
| 2 | 471 | 0.59 | 0.74 | 57 | empty |
| 3 | 335 | 0.54 | 0.74 | 42 | empty |
| 4 | 106 | 0.37 | 0.74 | 21 | empty |
| 5 | 79 | 0.33 | 0.75 | 25 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1883 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1869 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 991 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 269 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 259 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6AZM · Crystal structure of the 580 germline antibody bound to circumsporozoite protein NANP… · 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 6AZM · PDBe 6AZM
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