Research workbench
Crystal structure of neisseria meningitidis earp bound tdp
Analyse Crystal structure of neisseria meningitidis earp bound tdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F2A
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor P maturation arginine rhamnosyltransferase earp
- UniProt
- X5EQ00
- Ligands
- TYD, SO4
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Elongation factor P maturation arginine rhamnosyltransferase earp | protein | 376 | 43% helix, 18% strand | X5EQ00 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.87 | 0.88 | 126 | TYD |
| 2 | 62 | 0.70 | 0.96 | 19 | empty |
| 3 | 166 | 0.63 | 0.85 | 24 | empty |
| 4 | 124 | 0.60 | 0.85 | 18 | empty |
| 5 | 63 | 0.43 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–F · 1007 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7F2A · Crystal structure of Neisseria meningitidis EarP bound TDP · 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 X5EQ00
- Elsewhere: RCSB PDB 7F2A · PDBe 7F2A · UniProt X5EQ00
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