Research workbench
Crystal structure of human dihydropyrimidinease-like 2
Analyse Crystal structure of human dihydropyrimidinease-like 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GSE
- Type
- protein
- Length
- 1,901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 2
- EC
- 3.5.2.2
- UniProt
- Q16555
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dihydropyrimidinase-related protein 2 (EC 3.5.2.2) | protein | 475 | 36% helix, 24% strand | Q16555 |
| D | Dihydropyrimidinase-related protein 2 (EC 3.5.2.2) | protein | 476 | 36% helix, 24% strand | Q16555 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.86 | 0.89 | 78 | empty |
| 2 | 759 | 0.86 | 0.89 | 78 | empty |
| 3 | 425 | 0.74 | 0.84 | 34 | empty |
| 4 | 391 | 0.73 | 0.84 | 33 | empty |
| 5 | 212 | 0.66 | 0.85 | 32 | CA |
Interfaces
6 interfaces between chains.
- C–D · 1272 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1258 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1118 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1023 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GSE · Crystal Structure of Human Dihydropyrimidinease-like 2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · a predicted model of the same protein · chain B 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 Q16555
- Elsewhere: RCSB PDB 2GSE · PDBe 2GSE · UniProt Q16555
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