MolNFT v1 · #141302 · protein
Thdp-MN2+ complex of R395A variant of ecmend soaked with 2- ketoglutarate for 5 min
5Z2U: “Thdp-MN2+ complex of R395A variant of ecmend soaked with 2- ketoglutarate for 5 min”. X-ray diffraction, 3 ligands (TD6, TPP, MG). MolNFT v1 #141302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z2U
- Type
- protein
- Length
- 4,448 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P17109
- Ligands
- TD6, TPP, MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | — | protein | 556 | — | P17109 |
Ligands and binding sites
- TD6 · (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid · ligand · 7 copies · chains A, H, B, G, C, D, E, F
- TPP · Thiamine diphosphate · ligand · chains E, F
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 10 copies · chains B, C, D, E, F, G, H
- GOL · Glycerol · additive · 5 copies · chains C, D, G, H
- EDO · 1,2-ethanediol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5Z2U · ThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketoglutarate for 5 min · the same entry in another collection · chain H against H, TM-score 1.00
- P17109 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P17109
- Elsewhere: RCSB PDB 5Z2U · PDBe 5Z2U · UniProt P17109
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