Research workbench
Crystal structure of placental ribonuclease inhibitor in complex with human eosinophil derived neurotoxin at 2A resolution
Analyse Crystal structure of placental ribonuclease inhibitor in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BEX
- Type
- protein
- Length
- 1,183 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease inhibitor; Nonsecretory ribonuclease
- EC
- 3.1.27.5
- UniProt
- P13489, P10153
- Ligands
- MAK
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease inhibitor | protein | 456 | 41% helix, 13% strand | P13489 |
| B | Ribonuclease inhibitor | protein | 457 | 43% helix, 13% strand | P13489 |
| C, D | Nonsecretory ribonuclease (EC 3.1.27.5) | protein | 135 | 23% helix, 33% strand | P10153 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.77 | 0.87 | 46 | empty |
| 2 | 299 | 0.75 | 0.88 | 43 | empty |
| 3 | 138 | 0.66 | 0.88 | 33 | empty |
| 4 | 241 | 0.65 | 0.83 | 47 | empty |
| 5 | 272 | 0.58 | 0.79 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1848 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1454 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 381 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2BEX · Crystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil… · the same entry in another collection · chain A against A, TM-score 1.00
- P13489 · AlphaFold monomer V2.0 prediction for ribonuclease inhibitor (P13489) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P10153 · AlphaFold monomer V2.0 prediction for non-secretory ribonuclease (P10153) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P13489
- Every structure of UniProt P10153
- Elsewhere: RCSB PDB 2BEX · PDBe 2BEX · UniProt P13489 · UniProt P10153
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