MolNFT v1 · #122701 · protein
Crystal structure of sugar ABC transport system, substrate-binding protein from bordetella parapertussis 12822
5IX8 · Putative sugar ABC transport system, substrate-binding…: “Crystal structure of sugar ABC transport system, substrate-binding protein from bordetella parapertussis 12822”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best…
- PDB
- 5IX8
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar ABC transport system, substrate-binding protein
- UniProt
- Q7W6X1
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sugar ABC transport system, substrate-binding protein | protein | 318 | 39% helix, 17% strand | Q7W6X1 |
| B | Putative sugar ABC transport system, substrate-binding protein | protein | 321 | 38% helix, 17% strand | Q7W6X1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.58 | 0.75 | 43 | SO4 |
| 2 | 66 | 0.54 | 0.87 | 22 | EDO |
| 3 | 61 | 0.53 | 0.87 | 22 | EDO |
| 4 | 105 | 0.36 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 369 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 5IX8 · Crystal structure of sugar ABC transport system, substrate-binding protein from… · 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 Q7W6X1
- Elsewhere: RCSB PDB 5IX8 · PDBe 5IX8 · UniProt Q7W6X1
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