MolNFT v1 · #141297 · protein
Thdp-MN2+ complex of R413K variant of ecmend soaked with 2- ketoglutarate for 5 min
5Z2P · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Thdp-MN2+ complex of R413K variant of ecmend soaked with 2- ketoglutarate for 5 min”. X-ray diffraction, 2 ligands (TD6, MN), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5Z2P
- Type
- protein
- Length
- 4,448 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, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 556 | 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 · 8 copies · chains A, B, C, D, E, G, F, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 23 copies · chains A, B, C, D, E, F, H, G
- GOL · Glycerol · additive · 2 copies · chains D, G
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 | 606 | 0.85 | 0.90 | 100 | TD6, MN, FMT |
| 2 | 614 | 0.85 | 0.90 | 97 | FMT, TD6, MN |
| 3 | 615 | 0.85 | 0.90 | 99 | FMT, TD6, MN |
| 4 | 469 | 0.84 | 0.91 | 74 | TD6, MN |
| 5 | 605 | 0.82 | 0.87 | 93 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3499 Ų buried · 51 hydrogen bonds · protein-protein
- F–H · 3478 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3471 Ų buried · 51 hydrogen bonds · protein-protein
- E–G · 3426 Ų buried · 52 hydrogen bonds · protein-protein
- B–H · 1483 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5Z2P · ThDP-Mn2+ complex of R413K 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 5Z2P · PDBe 5Z2P · UniProt P17109
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