MolNFT v1 · #33879 · protein
Crystal structure of a probable GTP-binding protein engb
2CXX: “Crystal structure of a probable GTP-binding protein engb”. X-ray diffraction, 1 ligand (GDP), 10 pockets (best druggability 0.79). MolNFT v1 #33879 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2CXX
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable GTP-binding protein engb
- UniProt
- O57939
- Ligands
- GDP
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable GTP-binding protein engb | protein | 184 | 48% helix, 18% strand | O57939 |
| B | Probable GTP-binding protein engb | protein | 176 | 49% helix, 19% strand | O57939 |
| C | Probable GTP-binding protein engb | protein | 179 | 49% helix, 19% strand | O57939 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.79 | 0.80 | 90 | empty |
| 2 | 74 | 0.52 | 0.85 | 19 | empty |
| 3 | 154 | 0.46 | 0.76 | 19 | empty |
| 4 | 116 | 0.41 | 0.76 | 22 | empty |
| 5 | 92 | 0.40 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 464 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 404 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 150 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2CXX · Crystal structure of a probable GTP-binding protein engB · the same entry in another collection · chain A against A, TM-score 1.00
- O57939 · AlphaFold monomer V2.0 prediction for probable GTP-binding protein engb (O57939) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O57939
- Elsewhere: RCSB PDB 2CXX · PDBe 2CXX · UniProt O57939
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