MolNFT v1 · #47622 · protein
Complex of a camelid single-domain vhh antibody fragment with RNase a at 1.8A resolution: SE3-mono-2 crystal form with three se-met sites (M34, M51, M83) in vhh scaffold
2P42 · Ribonuclease pancreatic: “Complex of a camelid single-domain vhh antibody fragment with RNase a at 1.8A resolution: SE3-mono-2 crystal…”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.51). MolNFT v1 #47622 on…
- PDB
- 2P42
- 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
- MG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 14% 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 | 7% helix, 49% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.51 | 0.78 | 34 | MG |
| 2 | 57 | 0.32 | 0.77 | 15 | empty |
| 3 | 63 | 0.27 | 0.73 | 13 | empty |
| 4 | 56 | 0.25 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 610 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 607 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 349 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 modified (disulfide, engineered).
Compared structures
- 2P42 · Complex of a camelid single-domain vhh antibody fragment with RNASE A at 1.8A 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 2P42 · PDBe 2P42 · UniProt P61823
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