Research workbench
Crystal structure of the perchlorate reductase pcrab from azospira suillum ps
Analyse Crystal structure of the perchlorate reductase pcrab from azospira suillum ps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YDD
- Type
- protein
- Length
- 3,664 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, MO, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 895 | 33% helix, 17% strand | G8QM55 |
| B | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 329 | 26% helix, 17% strand | G8QM54 |
| C, E | Dmso reductase family type II enzyme, molybdopterin subunit | protein | 892 | 33% helix, 17% strand | G8QM55 |
| D, F | Dmso reductase family type II enzyme, iron-sulfur subunit | protein | 328 | 26% helix, 17% 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
- MO · Molybdenum atom · metal · 3 copies · chains A, C, E
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, E, C, F, D
- GOL · Glycerol · additive · chains C
- PEG · Di(hydroxyethyl)ether · 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 | 630 | 0.90 | 0.96 | 117 | SF4, MO, MGD, MD1 |
| 2 | 392 | 0.88 | 0.97 | 87 | SF4, MO, MGD |
| 3 | 396 | 0.88 | 0.96 | 84 | SF4, MO, MGD |
| 4 | 245 | 0.84 | 0.96 | 39 | MO, MD1 |
| 5 | 240 | 0.84 | 0.96 | 38 | MO, MD1 |
Interfaces
9 interfaces between chains.
- E–F · 4511 Ų buried · 87 hydrogen bonds · protein-protein
- C–D · 4493 Ų buried · 84 hydrogen bonds · protein-protein
- A–B · 4479 Ų buried · 83 hydrogen bonds · protein-protein
- C–E · 615 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 539 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4YDD · Crystal structure of the perchlorate reductase PcrAB from Azospira suillum PS · 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 4YDD · PDBe 4YDD · UniProt G8QM55 · UniProt G8QM54
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