Research workbench
Tyrosine ammonia-lyase from rhodobacter sphaeroides, complexed with caffeate
Analyse Tyrosine ammonia-lyase from rhodobacter sphaeroides, complexed with caffeate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O7D
- Type
- protein
- Length
- 4,114 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative histidine ammonia-lyase
- EC
- 4.3.1.-
- UniProt
- Q3IWB0
- Ligands
- DHC
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative histidine ammonia-lyase (EC 4.3.1.-) | protein | 515 | 56% helix, 7% strand | Q3IWB0 |
| C, D, E, F, G, H | Putative histidine ammonia-lyase (EC 4.3.1.-) | protein | 514 | 56% helix, 7% strand | Q3IWB0 |
Ligands and binding sites
- DHC · Caffeic acid · ligand · 8 copies · chains A, B, D, C, 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 | 297 | 0.81 | 0.92 | 54 | DHC |
| 2 | 274 | 0.80 | 0.92 | 53 | DHC |
| 3 | 148 | 0.80 | 0.97 | 34 | empty |
| 4 | 314 | 0.80 | 0.91 | 53 | DHC |
| 5 | 115 | 0.80 | 0.98 | 31 | DHC |
Interfaces
18 interfaces between chains.
- A–D · 4667 Ų buried · 69 hydrogen bonds · protein-protein
- F–G · 4666 Ų buried · 69 hydrogen bonds · protein-protein
- E–H · 4659 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 4656 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 3151 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 2O7D · Tyrosine ammonia-lyase from Rhodobacter sphaeroides, complexed with caffeate · the same entry in another collection · chain A against A, TM-score 1.00
- Q3IWB0 · AlphaFold monomer V2.0 prediction for tyrosine ammonia-lyase (Q3IWB0) · a predicted model of the same protein · 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 Q3IWB0
- Elsewhere: RCSB PDB 2O7D · PDBe 2O7D · UniProt Q3IWB0
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