MolNFT v1 · #95135 · protein
Crystal structure of probable mannonate dehydratase DD703_0947 (target efi-502222) from dickeya dadantii ECH703
4IHC · Mandelate RACEMASE/MUCONATE lactonizing protein: “Crystal structure of probable mannonate dehydratase DD703_0947 (target efi-502222) from dickeya dadantii…”. X-ray diffraction, 3 ligands (MG, IOD, CL), 20 pockets (best druggability…
- PDB
- 4IHC
- Type
- protein
- Length
- 3,162 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- C6CBG9
- Ligands
- MG, IOD, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 396 | 41% helix, 17% strand | C6CBG9 |
| B, C, D, E, F, H | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 395 | 41% helix, 16% strand | C6CBG9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- IOD · Iodide ion · ion · 19 copies · chains A, C, B, D, G, H, E, F
- CL · Chloride ion · ion · 9 copies · chains A, B, C, G, D, H, E, F
- GOL · Glycerol · additive · 14 copies · chains A, B, C, G, D, H, E, F
- FMT · Formic acid · additive · 9 copies · chains A, B, C, D, E, F, G, H
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 | 710 | 0.89 | 0.93 | 90 | CL, FMT, IOD |
| 2 | 694 | 0.89 | 0.93 | 83 | CL, IOD |
| 3 | 738 | 0.88 | 0.92 | 90 | CL, GOL, IOD |
| 4 | 680 | 0.88 | 0.93 | 81 | IOD, GOL |
| 5 | 675 | 0.88 | 0.92 | 78 | IOD |
Interfaces
17 interfaces between chains.
- A–B · 2634 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2622 Ų buried · 38 hydrogen bonds · protein-protein
- C–G · 2616 Ų buried · 39 hydrogen bonds · protein-protein
- D–H · 2605 Ų buried · 38 hydrogen bonds · protein-protein
- A–G · 1449 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4IHC · Crystal structure of probable mannonate dehydratase Dd703_0947 (target EFI-502222) from… · the same entry in another collection · chain H against H, TM-score 1.00
- C6CBG9 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member DD703_0947… · a predicted model of the same protein · chain F 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 C6CBG9
- Elsewhere: RCSB PDB 4IHC · PDBe 4IHC · UniProt C6CBG9
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