Research workbench
Crystal structure of human ornithine decarboxylase at 2.1 ångströms resolution
Analyse Crystal structure of human ornithine decarboxylase at 2.1 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D7K
- Type
- protein
- Length
- 819 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- P11926
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human ornithine decarboxylase (EC 4.1.1.17) | protein | 412 | 35% helix, 22% strand | P11926 |
| B | Human ornithine decarboxylase (EC 4.1.1.17) | protein | 407 | 35% helix, 22% strand | P11926 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.78 | 0.80 | 103 | empty |
| 2 | 942 | 0.78 | 0.80 | 74 | empty |
| 3 | 321 | 0.60 | 0.78 | 35 | empty |
| 4 | 87 | 0.53 | 0.85 | 23 | empty |
| 5 | 167 | 0.52 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 2886 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 1D7K · Crystal structure of human ornithine decarboxylase at 2.1 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P11926 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P11926) · a predicted model of the same protein · chain B 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 P11926
- Elsewhere: RCSB PDB 1D7K · PDBe 1D7K · UniProt P11926
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