Research workbench
Crystal structure of the perchlorate reductase pcrab mutant W461E of pcra from azospira suillum ps
Analyse Crystal structure of the perchlorate reductase pcrab mutant W461E of pcra from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E7O
- Type
- protein
- Length
- 7,344 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dmso reductase family type II enzyme, molybdopterin subunit; Dmso reductase family type…
- UniProt
- G8QM55, G8QM54
- Ligands
- SF4, MGD, MD1, F3S, MO
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 895 | 31% helix, 17% strand | G8QM55 |
| B, D, F, H, J, L | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 329 | 25% helix, 17% strand | G8QM54 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 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 · 6 copies · chains A, C, E, G, I, K
- MD1 · Phosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate ester · ligand · 6 copies · chains A, C, E, G, I, K
- F3S · FE3-S4 cluster · ligand · 6 copies · chains B, D, F, H, J, L
- MO · Molybdenum atom · metal · 6 copies · chains A, C, E, G, I, K
- EDO · 1,2-ethanediol · additive · 29 copies · chains A, B, E, F, C, D, G, H, I, J, K, L
- GOL · Glycerol · additive · 2 copies · chains A, C, E
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 | 617 | 0.90 | 0.97 | 110 | SF4, MO, MGD, MD1 |
| 2 | 622 | 0.90 | 0.96 | 108 | SF4, MO, MGD, MD1 |
| 3 | 596 | 0.90 | 0.96 | 108 | SF4, MO, MGD, MD1, EDO |
| 4 | 609 | 0.90 | 0.96 | 109 | SF4, MO, MGD, MD1 |
| 5 | 609 | 0.90 | 0.96 | 109 | SF4, MO, MGD, MD1 |
Interfaces
25 interfaces between chains.
- A–B · 4480 Ų buried · 86 hydrogen bonds · protein-protein
- C–D · 4474 Ų buried · 75 hydrogen bonds · protein-protein
- I–J · 4466 Ų buried · 78 hydrogen bonds · protein-protein
- G–H · 4464 Ų buried · 80 hydrogen bonds · protein-protein
- K–L · 4454 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 5E7O · Crystal structure of the perchlorate reductase PcrAB mutant W461E of PcrA from Azospira… · 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 G8QM55
- Every structure of UniProt G8QM54
- Elsewhere: RCSB PDB 5E7O · PDBe 5E7O · UniProt G8QM55 · UniProt G8QM54
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