MolNFT v1 · #158766 · protein
Crystal structure of yeast NRD1 cid in complex with SEN1 NIM3
6O3Y · Protein NRD1: “Crystal structure of yeast NRD1 cid in complex with SEN1 NIM3”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.63). MolNFT v1 #158766 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O3Y
- Type
- protein
- Length
- 450 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein NRD1; Helicase SEN1
- EC
- 3.6.4.-
- UniProt
- P53617, Q00416
- Ligands
- CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein NRD1 | protein | 147 | 80% helix, 0% strand | P53617 |
| B | Protein NRD1 | protein | 137 | 81% helix, 0% strand | P53617 |
| C | Protein NRD1 | protein | 146 | 79% helix, 0% strand | P53617 |
| D, F | Helicase SEN1 (EC 3.6.4.-) | protein | 7 | 0% helix, 0% strand | Q00416 |
| E | Helicase SEN1 (EC 3.6.4.-) | protein | 6 | 0% helix, 0% strand | Q00416 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.63 | 0.74 | 56 | empty |
| 2 | 99 | 0.55 | 0.84 | 29 | empty |
| 3 | 193 | 0.51 | 0.77 | 26 | empty |
| 4 | 82 | 0.34 | 0.75 | 17 | empty |
| 5 | 67 | 0.31 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 695 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 376 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 372 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 339 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6O3Y · Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 · the same entry in another collection · chain F against F, TM-score 1.00
- P53617 · AlphaFold monomer V2.0 prediction for protein NRD1 (P53617) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q00416 · AlphaFold monomer V2.0 prediction for helicase SEN1 (Q00416) · a predicted model of the same protein · chain E against A, TM-score 0.67
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 P53617
- Every structure of UniProt Q00416
- Elsewhere: RCSB PDB 6O3Y · PDBe 6O3Y · UniProt P53617 · UniProt Q00416
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