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The structure of the N-terminal domain of rsbr

Analyse The structure of the N-terminal domain of rsbr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BNL
Type: protein
Length: 778 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Modulator protein rsbr
UniProt: P42409
Ligands: NA
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Modulator protein rsbr	protein	129	78% helix, 0% strand	P42409
B	Modulator protein rsbr	protein	128	79% helix, 0% strand	P42409
C	Modulator protein rsbr	protein	134	77% helix, 0% strand	P42409

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains B, C, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.81	0.96	24	empty
2	162	0.81	0.96	23	empty
3	152	0.79	0.95	23	empty
4	173	0.47	0.76	26	NA
5	133	0.45	0.77	18	empty

Interfaces

5 interfaces between chains.

C–D · 1095 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1090 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1088 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 558 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 549 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2BNL · The structure of the N-terminal domain of RsbR · the same entry in another collection · chain F against F, TM-score 1.00
P42409 · AlphaFold monomer V2.0 prediction for rsbt co-antagonist protein rsbra (P42409) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P42409
Elsewhere: RCSB PDB 2BNL · PDBe 2BNL · UniProt P42409

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