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Crystal structure of thermostable fisufs-sufu complex from thermophilic fervidobacterium islandicum aw-1
Analyse Crystal structure of thermostable fisufs-sufu complex from thermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A6G
- Type
- protein
- Length
- 1,112 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase; Iron-sulfur cluster assembly scaffold protein nifu
- EC
- 2.8.1.7
- UniProt
- A0A1B0VPZ3, A0A1B0VLW5
- Ligands
- PLP, ZN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase (EC 2.8.1.7) | protein | 421 | 44% helix, 17% strand | A0A1B0VPZ3 |
| B | Cysteine desulfurase (EC 2.8.1.7) | protein | 422 | 43% helix, 17% strand | A0A1B0VPZ3 |
| C | Iron-sulfur cluster assembly scaffold protein nifu | protein | 136 | 47% helix, 13% strand | A0A1B0VLW5 |
| D | Iron-sulfur cluster assembly scaffold protein nifu | protein | 133 | 49% helix, 11% strand | A0A1B0VLW5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains C, A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.82 | 0.96 | 55 | PLP |
| 2 | 174 | 0.81 | 0.97 | 52 | PLP |
| 3 | 523 | 0.69 | 0.79 | 47 | empty |
| 4 | 507 | 0.69 | 0.79 | 36 | empty |
| 5 | 198 | 0.54 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3835 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 702 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 441 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 cofactor (oxidation, pyridoxal phosphate Schiff base).
Compared structures
- 6A6G · Crystal structure of thermostable FiSufS-SufU complex from thermophilic Fervidobacterium… · 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 A0A1B0VPZ3
- Every structure of UniProt A0A1B0VLW5
- Elsewhere: RCSB PDB 6A6G · PDBe 6A6G · UniProt A0A1B0VPZ3 · UniProt A0A1B0VLW5
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