Research workbench
Crystal structure of L-rhamnonate dehydratase from azotobacter vinelandii
Analyse Crystal structure of L-rhamnonate dehydratase from azotobacter vinelandii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OZ3
- Type
- protein
- Length
- 3,136 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- EC
- 4.2.1.90
- UniProt
- Q4J3N3
- Ligands
- NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 4.2.1.90) | protein | 396 | 40% helix, 17% strand | Q4J3N3 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 4.2.1.90) | protein | 388 | 36% helix, 18% strand | Q4J3N3 |
| D, G | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 4.2.1.90) | protein | 395 | 38% helix, 18% strand | Q4J3N3 |
| F | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 4.2.1.90) | protein | 387 | 40% helix, 18% strand | Q4J3N3 |
| H | Mandelate RACEMASE/MUCONATE lactonizing enzyme (EC 4.2.1.90) | protein | 383 | 38% helix, 18% strand | Q4J3N3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 31 copies · chains A, C, B, D, E, F, H, G
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 | 1146 | 0.83 | 0.84 | 106 | GOL |
| 2 | 1069 | 0.82 | 0.83 | 113 | GOL |
| 3 | 1126 | 0.82 | 0.83 | 116 | GOL |
| 4 | 1110 | 0.82 | 0.83 | 112 | GOL |
| 5 | 137 | 0.80 | 0.97 | 29 | empty |
Interfaces
13 interfaces between chains.
- G–H · 2522 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2507 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 2492 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 1708 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1689 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 120 modified (engineered).
Compared structures
- 2OZ3 · Crystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii · 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 Q4J3N3
- Elsewhere: RCSB PDB 2OZ3 · PDBe 2OZ3 · UniProt Q4J3N3
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