Research workbench
Crystal structure of the BD1-ntpr complex from BEND3 and pich
Analyse Crystal structure of the BD1-ntpr complex from BEND3 and pich in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JNO
- Type
- protein
- Length
- 154 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ben domain-containing protein 3; DNA excision repair protein ercc-6-like
- EC
- 3.6.4.12
- UniProt
- Q5T5X7, Q2NKX8
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ben domain-containing protein 3 | protein | 97 | 75% helix, 0% strand | Q5T5X7 |
| B | DNA excision repair protein ercc-6-like (EC 3.6.4.12) | protein | 57 | 67% helix, 0% strand | Q2NKX8 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.56 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JNO · Crystal structure of the BD1-NTPR complex from BEND3 and PICH · the same entry in another collection · chain A against A, TM-score 1.00
- Q5T5X7 · AlphaFold monomer V2.0 prediction for ben domain-containing protein 3 (Q5T5X7) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q2NKX8 · AlphaFold monomer V2.0 prediction for DNA excision repair protein ercc-6-like (Q2NKX8) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q5T5X7
- Every structure of UniProt Q2NKX8
- Elsewhere: RCSB PDB 5JNO · PDBe 5JNO · UniProt Q5T5X7 · UniProt Q2NKX8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.