Research workbench
1.50 ångströms resolution crystal structure of putative pterin binding protein prur (ATU3496) from agrobacterium fabrum str. C58
Analyse 1.50 ångströms resolution crystal structure of putative pterin binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KOS
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pterin binding protein
- UniProt
- A9CFB2
- Ligands
- GLC, NA
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pterin binding protein | protein | 149 | 23% helix, 34% strand | A9CFB2 |
| B, C | Pterin binding protein | protein | 148 | 21% helix, 36% strand | A9CFB2 |
| D | Pterin binding protein | protein | 146 | 24% helix, 38% strand | A9CFB2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- NA · Sodium ion · metal · 5 copies · chains A, C, D, B
- MLA · Malonic acid · additive · 6 copies · chains A, D, B, C
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.86 | 0.93 | 49 | NA |
| 2 | 398 | 0.57 | 0.75 | 46 | empty |
| 3 | 324 | 0.55 | 0.75 | 46 | NA |
| 4 | 54 | 0.29 | 0.75 | 14 | empty |
| 5 | 72 | 0.29 | 0.73 | 21 | MLA |
Interfaces
6 interfaces between chains.
- B–D · 624 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 594 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7KOS · 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR… · 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 A9CFB2
- Elsewhere: RCSB PDB 7KOS · PDBe 7KOS · UniProt A9CFB2
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