MolNFT v1 · #183427 · protein
Crystal structure of the coenzyme F420-dependent sulfite reductase from methanocaldococcus jannaschii at 2.3-a resolution
7NP8: “Crystal structure of the coenzyme F420-dependent sulfite reductase from methanocaldococcus jannaschii at…”. X-ray diffraction, 7 ligands (SF4, FAD, SRM), 20 pockets (best druggability 0.85). MolNFT v1 #183427 on GenesisL1: 3D…
- PDB
- 7NP8
- Type
- protein
- Length
- 2,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent sulfite reductase
- EC
- 1.8.98.3
- UniProt
- Q58280
- Ligands
- SF4, FAD, SRM, CA, FE, CL, SO3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Coenzyme F420-dependent sulfite reductase (EC 1.8.98.3) | protein | 619 | 34% helix, 23% strand | Q58280 |
| B, D | Coenzyme F420-dependent sulfite reductase (EC 1.8.98.3) | protein | 620 | 34% helix, 23% strand | Q58280 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 24 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SRM · Siroheme · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · chains D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- SO3 · Sulfite ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 32 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.85 | 0.86 | 111 | SF4, SRM, SO3 |
| 2 | 1154 | 0.84 | 0.85 | 118 | SF4, SO3, SRM |
| 3 | 1096 | 0.84 | 0.85 | 105 | SRM, GOL, SO3, SF4 |
| 4 | 1188 | 0.82 | 0.84 | 101 | SO3, SRM, GOL, CL, SF4 |
| 5 | 490 | 0.81 | 0.87 | 56 | FAD, MPD |
Interfaces
3 interfaces between chains.
- A–B · 3246 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 3192 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 670 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7NP8 · Crystal structure of the Coenzyme F420-dependent sulfite reductase from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q58280 · AlphaFold monomer V2.0 prediction for coenzyme F420-dependent sulfite reductase (Q58280) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q58280
- Elsewhere: RCSB PDB 7NP8 · PDBe 7NP8 · UniProt Q58280
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