MolNFT v1 · #118144 · protein
Structure of RNase a-K7H/R10H in complex with 3'-cmp
5ET4 · Ribonuclease pancreatic: “Structure of RNase a-K7H/R10H in complex with 3'-cmp”. X-ray diffraction, 1 ligand (C3P), 5 pockets (best druggability 0.63). MolNFT v1 #118144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ET4
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- C3P
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 36% strand | P61823 |
Ligands and binding sites
- C3P · Cytidine-3'-monophosphate · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.63 | 0.79 | 50 | C3P |
| 2 | 120 | 0.43 | 0.77 | 22 | empty |
| 3 | 117 | 0.41 | 0.76 | 26 | empty |
| 4 | 77 | 0.30 | 0.73 | 18 | C3P |
| 5 | 59 | 0.26 | 0.73 | 17 | C3P |
Interfaces
3 interfaces between chains.
- A–B · 964 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 176 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5ET4 · Structure of RNase A-K7H/R10H in complex with 3'-CMP · 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 5ET4 · PDBe 5ET4 · UniProt P61823
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