MolNFT v1 · #180087 · protein
1.50 ångströms resolution crystal structure of putative pterin binding protein prur (ATU3496) from agrobacterium fabrum str. C58
7KOS: “1.50 ångströms resolution crystal structure of putative pterin binding protein prur (ATU3496) from…”. X-ray diffraction, 2 ligands (GLC, NA), 7 pockets (best druggability 0.86). MolNFT v1 #180087 on GenesisL1: 3D structure, binding…
- 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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