Research workbench
Crystal structure of klebsiella pneumoniae rsta BEF3-activated N- terminal receiver domain
Analyse Crystal structure of klebsiella pneumoniae rsta BEF3-activated N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NIC
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding transcriptional regulator rsta
- UniProt
- G0GNT0
- Ligands
- BEF, MG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA-binding transcriptional regulator rsta | protein | 117 | 43% helix, 20% strand | G0GNT0 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.68 | 0.82 | 30 | empty |
| 2 | 333 | 0.66 | 0.81 | 29 | empty |
| 3 | 300 | 0.58 | 0.77 | 25 | empty |
| 4 | 211 | 0.50 | 0.76 | 32 | empty |
| 5 | 50 | 0.38 | 0.81 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 731 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 559 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 114 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4NIC · Crystal structure of Klebsiella pneumoniae RstA BeF3-activated N-terminal receiver domain · 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 G0GNT0
- Elsewhere: RCSB PDB 4NIC · PDBe 4NIC · UniProt G0GNT0
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