Research workbench
Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase
Analyse Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTK
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphobilinogen deaminase
- EC
- 2.5.1.61
- UniProt
- P06983
- Ligands
- DPM
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 294 | 39% helix, 24% strand | P06983 |
Ligands and binding sites
- DPM · 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.74 | 0.83 | 57 | DPM |
| 2 | 59 | 0.27 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1GTK · Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P06983 · AlphaFold monomer V2.0 prediction for porphobilinogen deaminase (P06983) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P06983
- Elsewhere: RCSB PDB 1GTK · PDBe 1GTK · UniProt P06983
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