Research workbench
Crystal structure of oxaloacetate decarboxylase from pseudomonas aeruginosa (PA4872) in complex with oxalate and MG2+.
Analyse Crystal structure of oxaloacetate decarboxylase from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8I
- Type
- protein
- Length
- 1,692 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PA4872 oxaloacetate decarboxylase
- EC
- 4.1.1.3
- UniProt
- Q9HUU1
- Ligands
- OXL, MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | PA4872 oxaloacetate decarboxylase (EC 4.1.1.3) | protein | 284 | 49% helix, 14% strand | Q9HUU1 |
| B | PA4872 oxaloacetate decarboxylase (EC 4.1.1.3) | protein | 283 | 48% helix, 14% strand | Q9HUU1 |
| C | PA4872 oxaloacetate decarboxylase (EC 4.1.1.3) | protein | 278 | 49% helix, 14% strand | Q9HUU1 |
| D | PA4872 oxaloacetate decarboxylase (EC 4.1.1.3) | protein | 280 | 49% helix, 14% strand | Q9HUU1 |
| E | PA4872 oxaloacetate decarboxylase (EC 4.1.1.3) | protein | 283 | 47% helix, 14% strand | Q9HUU1 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.86 | 0.93 | 49 | empty |
| 2 | 1049 | 0.82 | 0.83 | 75 | GOL |
| 3 | 1008 | 0.81 | 0.83 | 77 | GOL |
| 4 | 368 | 0.79 | 0.88 | 48 | empty |
| 5 | 425 | 0.77 | 0.86 | 52 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2224 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2198 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2182 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1453 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1442 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3B8I · Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9HUU1 · AlphaFold monomer V2.0 prediction for oxaloacetate decarboxylase (Q9HUU1) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9HUU1
- Elsewhere: RCSB PDB 3B8I · PDBe 3B8I · UniProt Q9HUU1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.