Research workbench
Crystal structure of dhdps from chlamydomonas reinhardtii
Analyse Crystal structure of dhdps from chlamydomonas reinhardtii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UI3
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- A8I3W3
- Ligands
- AKG
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Dihydrodipicolinate synthase | protein | 305 | 47% helix, 14% strand | A8I3W3 |
| C | Dihydrodipicolinate synthase | protein | 306 | 47% helix, 14% strand | A8I3W3 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.76 | 0.85 | 53 | empty |
| 2 | 364 | 0.76 | 0.86 | 47 | empty |
| 3 | 119 | 0.48 | 0.80 | 19 | empty |
| 4 | 97 | 0.46 | 0.80 | 19 | AKG |
| 5 | 111 | 0.46 | 0.79 | 23 | AKG |
Interfaces
5 interfaces between chains.
- B–C · 1708 Ų buried · 27 hydrogen bonds · protein-protein
- D–A · 1622 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 7 hydrogen bonds · protein-protein
- D–C · 669 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5UI3 · Crystal structure of DHDPS from chlamydomonas reinhardtii · the same entry in another collection · chain D against D, 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 A8I3W3
- Elsewhere: RCSB PDB 5UI3 · PDBe 5UI3 · UniProt A8I3W3
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