Research workbench
Dissimilatory nitrate reductase (nap) from desulfovibrio desulfuricans
Analyse Dissimilatory nitrate reductase (nap) from desulfovibrio desulfuricans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NAP
- Type
- protein
- Length
- 720 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (periplasmic nitrate reductase)
- Ligands
- MGD, SF4, MO
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (periplasmic nitrate reductase) | protein | 720 | 34% helix, 19% strand | — |
Ligands and binding sites
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 2 copies · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- MO · Molybdenum atom · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.88 | 0.96 | 81 | SF4, MO, MGD |
| 2 | 121 | 0.45 | 0.78 | 25 | MES |
| 3 | 74 | 0.33 | 0.75 | 14 | empty |
| 4 | 52 | 0.27 | 0.74 | 17 | empty |
Compared structures
- 2NAP · Dissimilatory nitrate reductase (nap) from desulfovibrio desulfuricans · 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
- Elsewhere: RCSB PDB 2NAP · PDBe 2NAP
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