Research workbench
Crystal structure of enolase superfamily member from bordetella bronchiseptica complexed with mg, M-xylarate and L-lyxarate
Analyse Crystal structure of enolase superfamily member from bordetella bronchiseptica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OZM
- Type
- protein
- Length
- 3,077 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mandelate racemase
- UniProt
- Q7WEE8
- Ligands
- DXL, LY9, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G | Putative mandelate racemase | protein | 386 | 40% helix, 19% strand | Q7WEE8 |
| D | Putative mandelate racemase | protein | 381 | 41% helix, 19% strand | Q7WEE8 |
| H | Putative mandelate racemase | protein | 380 | 41% helix, 18% strand | Q7WEE8 |
Ligands and binding sites
- DXL · D-xylaric acid · ligand · 6 copies · chains A, B, C, E, F, G
- LY9 · L-arabinaric acid · ligand · 2 copies · chains D, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 10 copies · chains A, B, H, C, E, D, G, F
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 | 297 | 0.84 | 0.95 | 43 | empty |
| 2 | 329 | 0.84 | 0.94 | 45 | empty |
| 3 | 321 | 0.84 | 0.93 | 44 | empty |
| 4 | 1181 | 0.83 | 0.84 | 107 | GOL |
| 5 | 892 | 0.78 | 0.81 | 76 | GOL |
Interfaces
16 interfaces between chains.
- A–G · 1948 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1928 Ų buried · 31 hydrogen bonds · protein-protein
- B–H · 1683 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1660 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1381 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3OZM · Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed… · the same entry in another collection · chain H against H, 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 Q7WEE8
- Elsewhere: RCSB PDB 3OZM · PDBe 3OZM · UniProt Q7WEE8
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