Research workbench
Crystal structure of the formolase FLS_V2 in space group P 21
Analyse Crystal structure of the formolase FLS_V2 in space group P 21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QPZ
- Type
- protein
- Length
- 4,497 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formolase
- UniProt
- Q9F4L3
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formolase | protein | 563 | 42% helix, 17% strand | Q9F4L3 |
| B, C, D, E, F, G, H | Formolase | protein | 562 | 44% helix, 17% strand | Q9F4L3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 626 | 0.79 | 0.84 | 95 | MG, TPP |
| 2 | 410 | 0.78 | 0.87 | 74 | MG, TPP |
| 3 | 556 | 0.78 | 0.85 | 94 | MG, TPP |
| 4 | 120 | 0.77 | 0.96 | 31 | TPP |
| 5 | 113 | 0.77 | 0.97 | 32 | MG, TPP |
Interfaces
16 interfaces between chains.
- E–F · 3487 Ų buried · 55 hydrogen bonds · protein-protein
- G–H · 3457 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3443 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3425 Ų buried · 45 hydrogen bonds · protein-protein
- F–G · 1288 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4QPZ · Crystal structure of the formolase FLS_v2 in space group P 21 · 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 Q9F4L3
- Elsewhere: RCSB PDB 4QPZ · PDBe 4QPZ · UniProt Q9F4L3
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