MolNFT v1 · #70169 · protein
NAB2:GFD1 complex
3LCN · Nuclear polyadenylated RNA-binding protein NAB2: “NAB2:GFD1 complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.52). MolNFT v1 #70169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LCN
- Type
- protein
- Length
- 240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear polyadenylated RNA-binding protein NAB2; MRNA transport factor GFD1
- UniProt
- P32505, Q04839
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear polyadenylated RNA-binding protein NAB2 | protein | 96 | 71% helix, 0% strand | P32505 |
| B | Nuclear polyadenylated RNA-binding protein NAB2 | protein | 97 | 72% helix, 0% strand | P32505 |
| C | MRNA transport factor GFD1 | protein | 25 | 92% helix, 0% strand | Q04839 |
| D | MRNA transport factor GFD1 | protein | 22 | 77% helix, 0% strand | Q04839 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.52 | 0.77 | 32 | empty |
| 2 | 78 | 0.33 | 0.74 | 16 | empty |
| 3 | 50 | 0.28 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 671 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 629 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3LCN · Nab2:Gfd1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P32505 · AlphaFold monomer V2.0 prediction for nuclear polyadenylated RNA- binding protein NAB2… · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q04839 · AlphaFold monomer V2.0 prediction for mRNA transport factor GFD1 (Q04839) · a predicted model of the same protein · chain C 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 P32505
- Every structure of UniProt Q04839
- Elsewhere: RCSB PDB 3LCN · PDBe 3LCN · UniProt P32505 · UniProt Q04839
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