Research workbench
Crystal structure of the C558(464)A/C559(465)A double mutant of TN501 mera in complex with NADPH and HG2+
Analyse Crystal structure of the C558(464)A/C559(465)A double mutant of TN501 mera in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K8D
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mercuric reductase
- EC
- 1.16.1.1
- UniProt
- P00392
- Ligands
- FAD, NDP, UNX, SO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mercuric reductase (EC 1.16.1.1) | protein | 466 | 33% helix, 26% strand | P00392 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- UNX · Unknown atom or ion · ion · 18 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.79 | 0.81 | 107 | SO4, FAD, NDP, UNX |
| 2 | 217 | 0.52 | 0.76 | 30 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4K8D · Crystal structure of the C558(464)A/C559(465)A double mutant of Tn501 MerA in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P00392 · AlphaFold monomer V2.0 prediction for mercuric reductase (P00392) · a predicted model of the same protein · 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 P00392
- Elsewhere: RCSB PDB 4K8D · PDBe 4K8D · UniProt P00392
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