MolNFT v1 · #102526 · protein
Crystal structure of the N-terminal domain of the legionella pneumophila protein sidc at 2.4A resolution
4OOJ · Sidc, interaptin: “Crystal structure of the N-terminal domain of the legionella pneumophila protein sidc at 2.4A resolution”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.78). MolNFT v1 #102526 on GenesisL1: 3D…
- PDB
- 4OOJ
- Type
- protein
- Length
- 2,433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sidc, interaptin
- UniProt
- Q5ZSK6
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sidc, interaptin | protein | 604 | 50% helix, 9% strand | Q5ZSK6 |
| B | Sidc, interaptin | protein | 608 | 50% helix, 10% strand | Q5ZSK6 |
| C | Sidc, interaptin | protein | 611 | 49% helix, 9% strand | Q5ZSK6 |
| D | Sidc, interaptin | protein | 610 | 50% helix, 9% strand | Q5ZSK6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.78 | 0.81 | 69 | empty |
| 2 | 600 | 0.78 | 0.84 | 67 | empty |
| 3 | 111 | 0.76 | 0.96 | 25 | MG, PEG |
| 4 | 484 | 0.76 | 0.84 | 59 | empty |
| 5 | 664 | 0.75 | 0.81 | 75 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2821 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2536 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 767 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OOJ · Crystal structure of the N-terminal domain of the Legionella pneumophila protein SidC at… · 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 Q5ZSK6
- Elsewhere: RCSB PDB 4OOJ · PDBe 4OOJ · UniProt Q5ZSK6
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