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The crystal structure of protein (XCC3681) from xanthomonas campestris pv. campestris str. atcc 33913
Analyse The crystal structure of protein (XCC3681) from xanthomonas campestris pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HIU
- Type
- protein
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8P4M6
- Ligands
- NA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 142 | 85% helix, 0% strand | Q8P4M6 |
| B | Uncharacterized protein | protein | 146 | 82% helix, 0% strand | Q8P4M6 |
| C | Uncharacterized protein | protein | 144 | 83% helix, 0% strand | Q8P4M6 |
| D | Uncharacterized protein | protein | 152 | 82% helix, 0% strand | Q8P4M6 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.60 | 0.76 | 46 | EDO |
| 2 | 117 | 0.42 | 0.76 | 24 | empty |
| 3 | 64 | 0.40 | 0.80 | 15 | EDO |
| 4 | 57 | 0.37 | 0.79 | 12 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1493 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1476 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3HIU · The crystal structure of protein (XCC3681) from Xanthomonas campestris pv. campestris… · 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 Q8P4M6
- Elsewhere: RCSB PDB 3HIU · PDBe 3HIU · UniProt Q8P4M6
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