Research workbench
Dihydroneopterin aldolase (dhna) from yersinia pestis co-crystallized with pterine
Analyse Dihydroneopterin aldolase (dhna) from yersinia pestis co-crystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OJO
- Type
- protein
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydroneopterin aldolase
- EC
- 4.1.2.25
- UniProt
- Q8CZR7
- Ligands
- PE0
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 7,8-dihydroneopterin aldolase (EC 4.1.2.25) | protein | 118 | 36% helix, 38% strand | Q8CZR7 |
| B | 7,8-dihydroneopterin aldolase (EC 4.1.2.25) | protein | 116 | 37% helix, 39% strand | Q8CZR7 |
Ligands and binding sites
- PE0 · Pterine · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.49 | 0.82 | 18 | PE0 |
| 2 | 108 | 0.47 | 0.79 | 27 | PE0 |
| 3 | 97 | 0.44 | 0.79 | 22 | PE0 |
| 4 | 90 | 0.44 | 0.79 | 19 | PE0 |
Interfaces
4 interfaces between chains.
- B–D · 991 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 985 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 980 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 975 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6OJO · Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine · the same entry in another collection · 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 Q8CZR7
- Elsewhere: RCSB PDB 6OJO · PDBe 6OJO · UniProt Q8CZR7
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