Research workbench
Crystal structure of NADP-bound nmra-area zinc finger complex
Analyse Crystal structure of NADP-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
- 2VUU
- Type
- protein
- Length
- 2,883 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
- NAP, ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 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, 19% strand | O59919 |
| B, D, G | Nitrogen metabolite repression regulator nmra | protein | 319 | 41% helix, 18% strand | O59919 |
| H | Nitrogen metabolite repression regulator nmra | protein | 319 | 43% helix, 19% strand | O59919 |
| I, J, K, L, M, N, P | Nitrogen regulatory protein area | protein | 42 | 24% helix, 10% strand | P17429 |
| O | Nitrogen regulatory protein area | protein | 41 | 24% helix, 10% strand | P17429 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.77 | 0.81 | 73 | NAP |
| 2 | 769 | 0.77 | 0.81 | 69 | NAP |
| 3 | 811 | 0.76 | 0.80 | 76 | NAP |
| 4 | 762 | 0.76 | 0.81 | 78 | NAP |
| 5 | 770 | 0.76 | 0.80 | 68 | NAP |
Interfaces
16 interfaces between chains.
- B–J · 843 Ų buried · 9 hydrogen bonds · protein-protein
- D–L · 798 Ų buried · 10 hydrogen bonds · protein-protein
- E–M · 773 Ų buried · 8 hydrogen bonds · protein-protein
- F–N · 771 Ų buried · 12 hydrogen bonds · protein-protein
- H–P · 770 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2VUU · Crystal structure of NADP-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 2VUU · PDBe 2VUU · UniProt O59919 · UniProt P17429
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