Research workbench
The crystal structure of bacillus cereus protein related to NIF3
Analyse The crystal structure of bacillus cereus protein related to NIF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GX8
- Type
- protein
- Length
- 1,084 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NIF3-related protein
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NIF3-related protein | protein | 359 | 35% helix, 34% strand | — |
| B | NIF3-related protein | protein | 361 | 35% helix, 35% strand | — |
| C | NIF3-related protein | protein | 364 | 34% helix, 34% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.70 | 0.83 | 33 | TRS, EPE |
| 2 | 232 | 0.69 | 0.86 | 34 | EPE |
| 3 | 246 | 0.68 | 0.84 | 28 | empty |
| 4 | 213 | 0.50 | 0.75 | 26 | empty |
| 5 | 115 | 0.41 | 0.76 | 19 | ZN |
Interfaces
3 interfaces between chains.
- A–B · 997 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 922 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 922 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2GX8 · The Crystal Structure of Bacillus cereus protein related to NIF3 · 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 2GX8 · PDBe 2GX8
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