Research workbench
Complex of a camelid single-domain vhh antibody fragment with RNase a at 2.3A resolution: SE5B-tetra crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.
Analyse Complex of a camelid single-domain vhh antibody fragment with RNase a at 2.3A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P48
- Type
- protein
- Length
- 245 residues
- Chains
- 2
- 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 0.25
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
| B | Antibody cab-RN05 | protein | 121 | 7% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 53 | 0.25 | 0.73 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 modified (disulfide, engineered).
Compared structures
- 2P48 · Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.3A resolution… · 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 2P48 · PDBe 2P48 · UniProt P61823
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