MolNFT v1 · #125220 · protein + RNA
NAB2 zn fingers 5-7 bound to A11G RNA
5L2L · NAB2P: “NAB2 zn fingers 5-7 bound to A11G RNA”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.90). MolNFT v1 #125220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L2L
- Type
- protein + RNA
- Length
- 334 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAB2P; RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
- UniProt
- A0A0C6D5P3
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAB2P | protein | 72 | 13% helix, 8% strand | A0A0C6D5P3 |
| B | NAB2P | protein | 74 | 12% helix, 8% strand | A0A0C6D5P3 |
| C, G, H | RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3') | rna | 10 | — | — |
| D | RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3') | rna | 11 | — | — |
| E | NAB2P | protein | 72 | 13% helix, 8% strand | A0A0C6D5P3 |
| F | NAB2P | protein | 75 | 12% helix, 8% strand | A0A0C6D5P3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 14 copies · chains A, G, B, E, F
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 | 1139 | 0.90 | 0.93 | 116 | empty |
| 2 | 114 | 0.46 | 0.79 | 14 | empty |
| 3 | 51 | 0.36 | 0.80 | 14 | empty |
Interfaces
20 interfaces between chains.
- B–C · 607 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 580 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–H · 572 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 569 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–G · 566 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5L2L · Nab2 Zn fingers 5-7 bound to A11G RNA · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0C6D5P3
- Elsewhere: RCSB PDB 5L2L · PDBe 5L2L · UniProt A0A0C6D5P3
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