MolNFT v1 · #90427 · protein
Crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase from burkholderia thailandensis
4EJ0: “Crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase from burkholderia thailandensis”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.84). MolNFT v1 #90427 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4EJ0
- Type
- protein
- Length
- 3,300 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-L-glycero-D-manno-heptose-6-epimerase
- EC
- 5.1.3.20
- UniProt
- Q2SY18
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | ADP-L-glycero-D-manno-heptose-6-epimerase (EC 5.1.3.20) | protein | 330 | 45% helix, 18% strand | Q2SY18 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.84 | 0.86 | 78 | NAP |
| 2 | 927 | 0.84 | 0.85 | 79 | NAP |
| 3 | 812 | 0.84 | 0.86 | 70 | NAP |
| 4 | 858 | 0.84 | 0.86 | 76 | NAP |
| 5 | 903 | 0.84 | 0.85 | 79 | NAP |
Interfaces
15 interfaces between chains.
- I–J · 910 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 910 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 903 Ų buried · 19 hydrogen bonds · protein-protein
- F–J · 902 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4EJ0 · Crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase from Burkholderia… · the same entry in another collection · chain J against J, TM-score 1.00
- Q2SY18 · AlphaFold monomer V2.0 prediction for ADP-L-glycero-D-manno- heptose-6-epimerase (Q2SY18) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q2SY18
- Elsewhere: RCSB PDB 4EJ0 · PDBe 4EJ0 · UniProt Q2SY18
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