MolNFT v1 · #107511 · protein
NMEDAH7PS R126S variant
4UCG · Phospho-2-dehydro-3-deoxyheptonate aldolase: “NMEDAH7PS R126S variant”. X-ray diffraction, 3 ligands (PEP, MN, SO4), 19 pockets (best druggability 0.71). MolNFT v1 #107511 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4UCG
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- Q9K169
- Ligands
- PEP, MN, SO4
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 336 | 41% helix, 17% strand | Q9K169 |
| B, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 41% helix, 17% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 335 | 42% helix, 17% strand | Q9K169 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.99 | 16 | empty |
| 2 | 65 | 0.71 | 0.96 | 21 | empty |
| 3 | 55 | 0.66 | 0.95 | 20 | empty |
| 4 | 79 | 0.62 | 0.91 | 22 | empty |
| 5 | 86 | 0.62 | 0.90 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2041 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1948 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 550 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 76 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UCG · NmeDAH7PS R126S variant · 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 Q9K169
- Elsewhere: RCSB PDB 4UCG · PDBe 4UCG · UniProt Q9K169
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