Research workbench
X-ray structure of a camelid affinity matured single-domain vhh antibody fragment in complex with RNase a
Analyse X-ray structure of a camelid affinity matured single-domain vhh antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P4A
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic; Antibody cab-RN05
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
| B, D | Antibody cab-RN05 | protein | 121 | 5% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.31 | 0.73 | 21 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 618 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 613 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2P4A · X-ray structure of a camelid affinity matured single-domain vhh antibody fragment in… · 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
- Every structure of UniProt P61823
- Elsewhere: RCSB PDB 2P4A · PDBe 2P4A · UniProt P61823
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