MolNFT v1 · #115356 · protein
Crystal structure of the perchlorate reductase pcrab - PHE164 gate switch intermediate - from azospira suillum ps
5CH7 · Dmso reductase family type II enzyme, molybdopterin subunit: “Crystal structure of the perchlorate reductase pcrab - PHE164 gate switch intermediate - from azospira…”. X-ray diffraction, 8 ligands (SF4, MGD, MD1), 20 pockets (best…
- PDB
- 5CH7
- Type
- protein
- Length
- 3,661 residues
- Chains
- 6
- 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, NA, MO, ZN, SO3
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 894 | 33% helix, 17% strand | G8QM55 |
| B | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 329 | 26% helix, 17% strand | G8QM54 |
| C | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 891 | 33% helix, 17% strand | G8QM55 |
| D | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 327 | 26% helix, 17% strand | G8QM54 |
| E | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 892 | 33% helix, 17% strand | G8QM55 |
| F | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 328 | 26% helix, 18% strand | G8QM54 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, B, C, D, E, F
- 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 · 3 copies · chains A, C, E
- 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 · 3 copies · chains A, C, E
- F3S · FE3-S4 cluster · ligand · 3 copies · chains B, D, F
- NA · Sodium ion · metal · 4 copies · chains A, C, E, F
- MO · Molybdenum atom · metal · 3 copies · chains A, C, E
- ZN · Zinc ion · metal · 3 copies · chains A, B, C, D, E, F
- SO3 · Sulfite ion · ion · 5 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, E, C, F, D
- GOL · Glycerol · additive · chains A, B
- ACT · Acetate ion · additive · chains C
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 | 594 | 0.90 | 0.96 | 109 | SF4, MO, MGD, MD1 |
| 2 | 390 | 0.88 | 0.97 | 86 | SF4, MO, MGD |
| 3 | 317 | 0.86 | 0.97 | 70 | SF4, MO, MGD |
| 4 | 241 | 0.84 | 0.96 | 42 | MO, MD1 |
| 5 | 243 | 0.84 | 0.96 | 41 | MO, MD1 |
Interfaces
9 interfaces between chains.
- C–D · 4501 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 4493 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 4492 Ų buried · 83 hydrogen bonds · protein-protein
- C–E · 599 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CH7 · Crystal structure of the perchlorate reductase PcrAB - Phe164 gate switch intermediate… · 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 5CH7 · PDBe 5CH7 · UniProt G8QM55 · UniProt G8QM54
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