Research workbench
Crystal structure of the coenzyme F420-dependent sulfite reductase from methanothermococcus thermolithotrophicus at 1.55-a resolution
Analyse Crystal structure of the coenzyme F420-dependent sulfite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NPA
- Type
- protein
- Length
- 9,878 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent sulfite reductase
- EC
- 1.8.98.3
- UniProt
- A0A2Z5PF12
- Ligands
- SF4, FAD, SRM, LI, SO4, CL, H2S
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, I, J | Coenzyme F420-dependent sulfite reductase (EC 1.8.98.3) | protein | 618 | 34% helix, 23% strand | A0A2Z5PF12 |
| D, E, H, K, L, M, O, P | Coenzyme F420-dependent sulfite reductase (EC 1.8.98.3) | protein | 617 | 34% helix, 23% strand | A0A2Z5PF12 |
| N | Coenzyme F420-dependent sulfite reductase (EC 1.8.98.3) | protein | 616 | 34% helix, 24% strand | A0A2Z5PF12 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 97 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- FAD · Flavin-adenine dinucleotide · ligand · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- SRM · Siroheme · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- LI · Lithium ion · metal · 4 copies · chains A, C, F, H, J, L, N, P
- SO4 · Sulfate ion · ion · 31 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, P, N, O
- CL · Chloride ion · ion · 29 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- H2S · Hydrosulfuric acid · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- EDO · 1,2-ethanediol · additive · 123 copies · chains A, B, D, C, E, F, H, G, I, J, O, P, L, K, M, N
- GOL · Glycerol · additive · 19 copies · chains A, B, C, E, F, G, I, J, L, K, M, P, N, O
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains C, D, K, L, M, N, O
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains H, I, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.86 | 0.87 | 111 | SRM, EDO, SO4, H2S, SF4 |
| 2 | 983 | 0.86 | 0.87 | 114 | SRM, SO4, H2S, SF4, EDO |
| 3 | 545 | 0.85 | 0.91 | 69 | FAD |
| 4 | 556 | 0.85 | 0.91 | 70 | FAD |
| 5 | 936 | 0.85 | 0.87 | 117 | SF4, EDO, SRM, SO4, H2S |
Interfaces
33 interfaces between chains.
- K–L · 3276 Ų buried · 52 hydrogen bonds · protein-protein
- I–J · 3239 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 3224 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3209 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3207 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 7NPA · Crystal structure of the Coenzyme F420-dependent sulfite reductase from… · 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 A0A2Z5PF12
- Elsewhere: RCSB PDB 7NPA · PDBe 7NPA · UniProt A0A2Z5PF12
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.