Research workbench
Crystal structure of dihydroneopterin aldolase from bacillus anthracis complex with 9-methylguanine
Analyse Crystal structure of dihydroneopterin aldolase from bacillus anthracis complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FAR
- Type
- protein
- Length
- 956 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydroneopterin aldolase
- EC
- 4.1.2.25
- UniProt
- J7VEZ6
- Ligands
- 9MG
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydroneopterin aldolase (EC 4.1.2.25) | protein | 118 | 33% helix, 32% strand | J7VEZ6 |
| B, E | 7,8-dihydroneopterin aldolase (EC 4.1.2.25) | protein | 119 | 36% helix, 34% strand | J7VEZ6 |
| C, D, F, G, H | 7,8-dihydroneopterin aldolase (EC 4.1.2.25) | protein | 120 | 34% helix, 33% strand | J7VEZ6 |
Ligands and binding sites
- 9MG · 9-methylguanine · ligand · 8 copies · chains A, D, B, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.99 | 21 | empty |
| 2 | 68 | 0.74 | 0.98 | 23 | empty |
| 3 | 77 | 0.73 | 0.97 | 24 | empty |
| 4 | 72 | 0.73 | 0.98 | 24 | empty |
| 5 | 1098 | 0.69 | 0.74 | 107 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1061 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1050 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1049 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1044 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 5FAR · Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complex with… · the same entry in another collection · chain E against E, 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 J7VEZ6
- Elsewhere: RCSB PDB 5FAR · PDBe 5FAR · UniProt J7VEZ6
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