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Crystal structure of the N-terminal domain of E.COLI ybgf

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

PDB: 2XDJ
Type: protein
Length: 396 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein ybgf
UniProt: P45955
Ligands: NA
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein ybgf	protein	66	94% helix, 0% strand	P45955
B, D, E	Uncharacterized protein ybgf	protein	67	94% helix, 0% strand	P45955
C	Uncharacterized protein ybgf	protein	67	96% helix, 0% strand	P45955
F	Uncharacterized protein ybgf	protein	62	94% helix, 0% strand	P45955

Ligands and binding sites

NA · Sodium ion · metal · chains C, D, E
ACT · Acetate ion · additive · chains A, B, F

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.32	0.73	12	empty

Interfaces

8 interfaces between chains.

C–E · 1424 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1407 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 1385 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1345 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 1317 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2XDJ · Crystal structure of the N-terminal domain of E.coli YbgF · the same entry in another collection · chain F against F, TM-score 1.00
P45955 · AlphaFold monomer V2.0 prediction for cell division coordinator cpob (P45955) · a predicted model of the same protein · chain B against A, TM-score 0.87

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 P45955
Elsewhere: RCSB PDB 2XDJ · PDBe 2XDJ · UniProt P45955

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