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Crystal structure of TOLB/PAL complex from yersinia pestis.

Analyse Crystal structure of TOLB/PAL complex from yersinia pestis. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R40
Type: protein
Length: 1,059 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein tolb; Peptidoglycan-associated lipoprotein
UniProt: Q8ZGZ1, Q7CH55
Ligands: SO4
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein tolb	protein	406	10% helix, 46% strand	Q8ZGZ1
B, D	Peptidoglycan-associated lipoprotein	protein	124	43% helix, 15% strand	Q7CH55
C	Protein tolb	protein	405	9% helix, 45% strand	Q8ZGZ1

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains B, C
FMT · Formic acid · additive · 2 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	452	0.82	0.90	40	empty
2	463	0.81	0.88	39	empty
3	671	0.77	0.83	85	FMT, SO4
4	51	0.71	0.98	19	empty
5	56	0.71	0.97	18	empty

Interfaces

5 interfaces between chains.

A–B · 1232 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1161 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 395 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 356 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 246 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4R40 · Crystal Structure of TolB/Pal complex from Yersinia pestis. · the same entry in another collection · chain A against A, TM-score 1.00
Q8ZGZ1 · AlphaFold monomer V2.0 prediction for tol-pal system protein tolb (Q8ZGZ1) · 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 Q8ZGZ1
Every structure of UniProt Q7CH55
Elsewhere: RCSB PDB 4R40 · PDBe 4R40 · UniProt Q8ZGZ1 · UniProt Q7CH55

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