Research workbench
Complex of a dromedary single-domain vhh antibody fragment with RNase a
Analyse Complex of a dromedary single-domain vhh antibody fragment with RNase a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BZQ
- Type
- protein
- Length
- 992 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (RNase a); Protein (antibody cab-RN05)
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (RNase a) (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
| K, L, M, N | Protein (antibody cab-RN05) | protein | 124 | 5% helix, 47% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
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 | 964 | 0.71 | 0.75 | 76 | PO4 |
| 2 | 403 | 0.58 | 0.75 | 42 | PO4 |
| 3 | 241 | 0.53 | 0.76 | 26 | empty |
| 4 | 210 | 0.48 | 0.75 | 23 | empty |
| 5 | 111 | 0.43 | 0.77 | 17 | empty |
Interfaces
13 interfaces between chains.
- B–N · 602 Ų buried · 8 hydrogen bonds · protein-protein
- C–M · 591 Ų buried · 10 hydrogen bonds · protein-protein
- D–K · 591 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 580 Ų buried · 8 hydrogen bonds · protein-protein
- D–M · 278 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 1BZQ · Complex of a dromedary single-domain vhh antibody fragment with RNase a · 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 1BZQ · PDBe 1BZQ · UniProt P61823
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