Research workbench
Ensemble refinement of the protein crystal structure of human ribonuclease inhibitor complexed with ribonuclease I
Analyse Ensemble refinement of the protein crystal structure of human ribonuclease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q4G
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic; Ribonuclease inhibitor
- EC
- 3.1.27.5
- UniProt
- P07998, P13489
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Z | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 126 | 19% helix, 37% strand | P07998 |
| W, Y | Ribonuclease inhibitor | protein | 460 | 41% helix, 14% strand | P13489 |
Ligands and binding sites
- CIT · Citric acid · additive · chains X, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.72 | 0.80 | 72 | empty |
| 2 | 653 | 0.71 | 0.79 | 67 | empty |
| 3 | 191 | 0.71 | 0.88 | 33 | empty |
| 4 | 623 | 0.70 | 0.79 | 65 | empty |
| 5 | 313 | 0.70 | 0.84 | 49 | empty |
Interfaces
5 interfaces between chains.
- W–Y · 1755 Ų buried · 29 hydrogen bonds · protein-protein
- X–W · 1541 Ų buried · 22 hydrogen bonds · protein-protein
- Z–Y · 1486 Ų buried · 23 hydrogen bonds · protein-protein
- W–Z · 96 Ų buried · 3 hydrogen bonds · protein-protein
- X–Y · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2Q4G · Ensemble refinement of the protein crystal structure of human ribonuclease inhibitor… · the same entry in another collection · chain X against X, TM-score 1.00
- P13489 · AlphaFold monomer V2.0 prediction for ribonuclease inhibitor (P13489) · a predicted model of the same protein · chain W against A, TM-score 0.99
- P07998 · AlphaFold monomer V2.0 prediction for ribonuclease pancreatic (P07998) · a predicted model of the same protein · chain X against A, TM-score 0.97
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
- Every structure of UniProt P13489
- Elsewhere: RCSB PDB 2Q4G · PDBe 2Q4G · UniProt P07998 · UniProt P13489
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