Research workbench
The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase
Analyse The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EQ2
- Type
- protein
- Length
- 2,970 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-L-glycero-D-mannoheptose 6-epimerase
- EC
- 5.1.3.20
- UniProt
- P67910
- Ligands
- NAP, ADQ
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) | protein | 273 | 47% helix, 16% strand | P67910 |
| B, E, J | ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) | protein | 300 | 45% helix, 17% strand | P67910 |
| C | ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) | protein | 272 | 47% helix, 17% strand | P67910 |
| D, F, G, I | ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) | protein | 307 | 45% helix, 17% strand | P67910 |
| H | ADP-L-glycero-D-mannoheptose 6-epimerase (EC 5.1.3.20) | protein | 297 | 46% helix, 16% strand | P67910 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- ADQ · Adenosine-5'-diphosphate-glucose · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.83 | 0.86 | 69 | NAP, ADQ |
| 2 | 768 | 0.83 | 0.86 | 73 | NAP, ADQ |
| 3 | 789 | 0.83 | 0.86 | 70 | NAP, ADQ |
| 4 | 971 | 0.82 | 0.83 | 72 | NAP, ADQ |
| 5 | 771 | 0.79 | 0.83 | 66 | NAP, ADQ |
Interfaces
12 interfaces between chains.
- H–I · 800 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 799 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 793 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 790 Ų buried · 13 hydrogen bonds · protein-protein
- G–J · 787 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (oxidation).
Compared structures
- 1EQ2 · The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase · the same entry in another collection · chain J against J, TM-score 1.00
- P67910 · AlphaFold monomer V2.0 prediction for ADP-L-glycero-D-manno- heptose-6-epimerase (P67910) · a predicted model of the same protein · chain D 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 P67910
- Elsewhere: RCSB PDB 1EQ2 · PDBe 1EQ2 · UniProt P67910
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