Research workbench
Crystal structure of lactobacillus farciminis oxalate decarboxylase formate complex
Analyse Crystal structure of lactobacillus farciminis oxalate decarboxylase formate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L9I
- Type
- protein
- Length
- 2,028 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalate decarboxylase
- UniProt
- A0A0H4LHD1
- Ligands
- MN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Oxalate decarboxylase | protein | 338 | 15% helix, 41% strand | A0A0H4LHD1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D, E, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.73 | 0.77 | 111 | empty |
| 2 | 1029 | 0.73 | 0.77 | 116 | empty |
| 3 | 967 | 0.73 | 0.77 | 113 | empty |
| 4 | 373 | 0.58 | 0.76 | 41 | empty |
| 5 | 324 | 0.57 | 0.76 | 34 | empty |
Interfaces
9 interfaces between chains.
- C–E · 2323 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 2303 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 2289 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 2281 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 2257 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6L9I · Crystal Structure of Lactobacillus farciminis Oxalate Decarboxylase Formate Complex · 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 A0A0H4LHD1
- Elsewhere: RCSB PDB 6L9I · PDBe 6L9I · UniProt A0A0H4LHD1
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