Research workbench
Thdp-MN2+ complex of R395K variant of ecmend soaked with 2- ketoglutarate for 5 min
Analyse Thdp-MN2+ complex of R395K variant of ecmend soaked with 2- ketoglutarate for 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z2R
- Type
- protein
- Length
- 4,447 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
- EC
- 2.2.1.9
- UniProt
- P17109
- Ligands
- TD6, TPP, MG, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 556 | 40% helix, 16% strand | P17109 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 555 | 41% helix, 16% strand | 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, B, C, D, E, F, G, H
- TPP · Thiamine diphosphate · ligand · chains E, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, H
- MN · Manganese (II) ion · metal · chains G
- FMT · Formic acid · additive · 29 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 717 | 0.85 | 0.89 | 112 | TD6 |
| 2 | 374 | 0.82 | 0.90 | 55 | FMT, TD6, MG |
| 3 | 754 | 0.81 | 0.85 | 79 | TPP, FMT |
| 4 | 717 | 0.81 | 0.85 | 78 | TD6 |
| 5 | 837 | 0.81 | 0.84 | 85 | TD6, FMT |
Interfaces
15 interfaces between chains.
- G–H · 3511 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3507 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3491 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3485 Ų buried · 50 hydrogen bonds · protein-protein
- F–H · 1505 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5Z2R · ThDP-Mn2+ complex of R395K 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 C 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 5Z2R · PDBe 5Z2R · UniProt P17109
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