Research workbench

Salmonella global domain 245

Analyse Salmonella global domain 245 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I5D
Type: protein
Length: 1,359 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inner membrane protein yejm
UniProt: P40709
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inner membrane protein yejm	protein	339	37% helix, 20% strand	P40709
B	Inner membrane protein yejm	protein	340	36% helix, 20% strand	P40709
C	Inner membrane protein yejm	protein	338	37% helix, 20% strand	P40709
D	Inner membrane protein yejm	protein	342	37% helix, 21% strand	P40709

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	828	0.69	0.75	61	empty
2	469	0.67	0.79	39	empty
3	406	0.64	0.78	35	empty
4	77	0.62	0.91	27	empty
5	298	0.58	0.77	47	empty

Interfaces

5 interfaces between chains.

B–D · 459 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 273 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 208 Å² buried · 1 hydrogen bond · protein-protein
A–B · 85 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 26 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

5I5D · Salmonella global domain 245 · the same entry in another collection · chain D against D, TM-score 1.00
P40709 · AlphaFold monomer V2.0 prediction for inner membrane protein yejm (P40709) · a predicted model of the same protein · chain C 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 P40709
Elsewhere: RCSB PDB 5I5D · PDBe 5I5D · UniProt P40709

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