Research workbench
Crystal structure of a GTP-binding protein enga (der homolog) from neisseria gonorrhoeae bound to GDP
Analyse Crystal structure of a GTP-binding protein enga (der homolog) from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XRS
- Type
- protein
- Length
- 1,560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase der
- Ligands
- GDP, CL, IOD
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase der | protein | 388 | 37% helix, 23% strand | — |
| B | GTPase der | protein | 392 | 37% helix, 23% strand | — |
| C | GTPase der | protein | 388 | 38% helix, 24% strand | — |
| D | GTPase der | protein | 392 | 36% helix, 23% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, D, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.71 | 0.78 | 72 | empty |
| 2 | 630 | 0.70 | 0.79 | 55 | empty |
| 3 | 571 | 0.67 | 0.77 | 45 | empty |
| 4 | 467 | 0.65 | 0.78 | 66 | GDP |
| 5 | 396 | 0.60 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1650 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1607 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XRS · Crystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae… · 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
- Elsewhere: RCSB PDB 6XRS · PDBe 6XRS
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