MolNFT v1 · #32059 · protein
Crystal structure of placental ribonuclease inhibitor in complex with human eosinophil derived neurotoxin at 2A resolution
2BEX: “Crystal structure of placental ribonuclease inhibitor in complex with human eosinophil derived neurotoxin at…”. X-ray diffraction, 1 ligand (MAK), 10 pockets (best druggability 0.77). MolNFT v1 #32059 on GenesisL1: 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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