Research workbench
Crystal structure of NAD-bound nmra-area zinc finger complex
Analyse Crystal structure of NAD-bound nmra-area zinc finger complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VUT
- Type
- protein
- Length
- 2,884 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen metabolite repression regulator nmra; Nitrogen regulatory protein area
- UniProt
- O59919, P17429
- Ligands
- NAD, ZN, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Nitrogen metabolite repression regulator nmra | protein | 318 | 43% helix, 18% strand | O59919 |
| B, D | Nitrogen metabolite repression regulator nmra | protein | 320 | 43% helix, 18% strand | O59919 |
| G | Nitrogen metabolite repression regulator nmra | protein | 319 | 41% helix, 19% strand | O59919 |
| H | Nitrogen metabolite repression regulator nmra | protein | 319 | 42% helix, 18% strand | O59919 |
| I, J, L, M, N, P | Nitrogen regulatory protein area | protein | 42 | 24% helix, 10% strand | P17429 |
| K, O | Nitrogen regulatory protein area | protein | 41 | 24% helix, 15% strand | P17429 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, K, B, C, D, I, E, F, G, H, O
- ZN · Zinc ion · metal · 8 copies · chains I, J, K, L, M, N, O, P
- CL · Chloride ion · ion · 7 copies · chains A, C, D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains C, K, G, O, E, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.78 | 0.80 | 96 | CL, NAD |
| 2 | 920 | 0.78 | 0.80 | 91 | NAD, CL |
| 3 | 682 | 0.77 | 0.82 | 65 | NAD |
| 4 | 820 | 0.76 | 0.80 | 74 | NAD |
| 5 | 783 | 0.76 | 0.80 | 72 | NAD |
Interfaces
23 interfaces between chains.
- B–J · 857 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 830 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 828 Ų buried · 10 hydrogen bonds · protein-protein
- F–N · 818 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 814 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2VUT · Crystal structure of NAD-bound NmrA-AreA zinc finger complex · the same entry in another collection · chain P against P, 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 O59919
- Every structure of UniProt P17429
- Elsewhere: RCSB PDB 2VUT · PDBe 2VUT · UniProt O59919 · UniProt P17429
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