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Crystal structure of urta from synechococcus CC9311 in complex with urea and calcium
Analyse Crystal structure of urta from synechococcus CC9311 in complex with urea and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6E
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urea ABC transporter, periplasmic urea-binding protein
- UniProt
- Q0I663
- Ligands
- URE, CA, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urea ABC transporter, periplasmic urea-binding protein | protein | 397 | 39% helix, 23% strand | Q0I663 |
| B | Urea ABC transporter, periplasmic urea-binding protein | protein | 400 | 38% helix, 23% strand | Q0I663 |
Ligands and binding sites
- URE · Urea · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 12 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.80 | 0.87 | 53 | CA |
| 2 | 109 | 0.39 | 0.75 | 22 | empty |
| 3 | 96 | 0.37 | 0.75 | 23 | empty |
| 4 | 69 | 0.33 | 0.76 | 15 | CA |
| 5 | 77 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7S6E · Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium · 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 Q0I663
- Elsewhere: RCSB PDB 7S6E · PDBe 7S6E · UniProt Q0I663
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