MolNFT v1 · #98047 · protein
The X-ray crystal structure of a dimeric variant of human pancreatic ribonuclease
4KXH · Ribonuclease pancreatic: “The X-ray crystal structure of a dimeric variant of human pancreatic ribonuclease”. X-ray diffraction, 3 ligands (NA, SO4, CL), 6 pockets (best druggability 0.81). MolNFT v1 #98047 on GenesisL1: 3D…
- PDB
- 4KXH
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic
- EC
- 3.1.27.5
- UniProt
- P07998
- Ligands
- NA, SO4, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 120 | 26% helix, 38% strand | P07998 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.81 | 0.82 | 104 | NA, SO4 |
| 2 | 91 | 0.43 | 0.79 | 24 | empty |
| 3 | 67 | 0.39 | 0.79 | 14 | empty |
| 4 | 71 | 0.36 | 0.78 | 21 | empty |
| 5 | 101 | 0.36 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1635 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1532 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 500 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4KXH · The X-ray crystal structure of a dimeric variant of human pancreatic ribonuclease · the same entry in another collection · chain B against B, TM-score 1.00
- P07998 · AlphaFold monomer V2.0 prediction for ribonuclease pancreatic (P07998) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P07998
- Elsewhere: RCSB PDB 4KXH · PDBe 4KXH · UniProt P07998
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