MolNFT v1 · #139408 · protein
Crystal structure of HCP2 from salmonella typhimurium
5XEU · HCP1 family type VI secretion system effector: “Crystal structure of HCP2 from salmonella typhimurium”. X-ray diffraction, 6 pockets (best druggability 0.39). MolNFT v1 #139408 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5XEU
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCP1 family type VI secretion system effector
- UniProt
- H9L4J8
- Pockets
- 6 · best druggability 0.39
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCP1 family type VI secretion system effector | protein | 128 | 9% helix, 52% strand | H9L4J8 |
| B | HCP1 family type VI secretion system effector | protein | 128 | 9% helix, 55% strand | H9L4J8 |
| C | HCP1 family type VI secretion system effector | protein | 129 | 9% helix, 53% strand | H9L4J8 |
| D | HCP1 family type VI secretion system effector | protein | 129 | 8% helix, 57% strand | H9L4J8 |
| E, F | HCP1 family type VI secretion system effector | protein | 128 | 8% helix, 56% strand | H9L4J8 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.39 | 0.76 | 18 | empty |
| 2 | 97 | 0.39 | 0.76 | 27 | empty |
| 3 | 92 | 0.37 | 0.75 | 20 | empty |
| 4 | 78 | 0.36 | 0.76 | 17 | empty |
| 5 | 81 | 0.30 | 0.73 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1007 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1004 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 991 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 981 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 980 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5XEU · crystal structure of Hcp2 from Salmonella typhimurium · 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 H9L4J8
- Elsewhere: RCSB PDB 5XEU · PDBe 5XEU · UniProt H9L4J8
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