Research workbench
Crystal structure analysis of the anti-arsonate germline antibody 36- 65 in complex with a phage display derived dodecapeptide rlliadppspre
Analyse Crystal structure analysis of the anti-arsonate germline antibody 36- 65 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A6D
- Type
- protein
- Length
- 877 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline antibody 36-65 Fab light chain; Germline antibody 36-65 Fab heavy chain…
- Pockets
- 9 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Germline antibody 36-65 Fab light chain | protein | 214 | 7% helix, 48% strand | — |
| H | Germline antibody 36-65 Fab heavy chain | protein | 218 | 6% helix, 50% strand | — |
| B | Germline antibody 36-65 Fab heavy chain | protein | 219 | 5% helix, 51% strand | — |
| P | Dodecapeptide, rlliadppspre | protein | 12 | 0% helix, 0% strand | — |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.52 | 0.74 | 42 | empty |
| 2 | 259 | 0.50 | 0.74 | 45 | empty |
| 3 | 128 | 0.41 | 0.75 | 25 | empty |
| 4 | 110 | 0.37 | 0.74 | 24 | empty |
| 5 | 70 | 0.36 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1899 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 17 hydrogen bonds · protein-protein
- A–P · 268 Ų buried · 8 hydrogen bonds · protein-protein
- B–P · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2A6D · Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a… · 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
- Elsewhere: RCSB PDB 2A6D · PDBe 2A6D
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