MolNFT v1 · #185225 · protein
Caulobacter crescentus xylonolactonase with D-xylose, P21 space group
7PLC · Smp-30/CGR1 family protein: “Caulobacter crescentus xylonolactonase with D-xylose, P21 space group”. X-ray diffraction, 4 ligands (XYP, XYS, FE2), 17 pockets (best druggability 0.79). MolNFT v1 #185225 on GenesisL1: 3D structure…
- PDB
- 7PLC
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smp-30/CGR1 family protein
- EC
- 3.1.1.68
- UniProt
- Q9A9Z1
- Ligands
- XYP, XYS, FE2, SO4
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Smp-30/CGR1 family protein (EC 3.1.1.68) | protein | 286 | 3% helix, 56% strand | Q9A9Z1 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, D, B, C
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, C
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.79 | 0.96 | 30 | empty |
| 2 | 134 | 0.77 | 0.95 | 26 | empty |
| 3 | 126 | 0.77 | 0.95 | 28 | empty |
| 4 | 133 | 0.75 | 0.94 | 30 | empty |
| 5 | 343 | 0.61 | 0.78 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 672 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 468 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 417 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PLC · Caulobacter crescentus xylonolactonase with D-xylose, P21 space group · 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 Q9A9Z1
- Elsewhere: RCSB PDB 7PLC · PDBe 7PLC · UniProt Q9A9Z1
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