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Crystal structure of spab basal pilin from lactobacillus rhamnosus gg

Analyse Crystal structure of spab basal pilin from lactobacillus rhamnosus gg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CBS
Type: protein
Length: 991 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lpxtg cell wall anchor domain-containing protein
UniProt: A0A5P5Z9C8
Ligands: MG, CL
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 8 distinct chains · 20% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lpxtg cell wall anchor domain-containing protein	protein	132	20% helix, 39% strand	A0A5P5Z9C8
B	Lpxtg cell wall anchor domain-containing protein	protein	131	20% helix, 38% strand	A0A5P5Z9C8
C	Lpxtg cell wall anchor domain-containing protein	protein	130	20% helix, 38% strand	A0A5P5Z9C8
D	Lpxtg cell wall anchor domain-containing protein	protein	126	18% helix, 40% strand	A0A5P5Z9C8
E	Lpxtg cell wall anchor domain-containing protein	protein	121	21% helix, 38% strand	A0A5P5Z9C8
G	Lpxtg cell wall anchor domain-containing protein	protein	127	18% helix, 38% strand	A0A5P5Z9C8
F	Lpxtg cell wall anchor domain-containing protein	protein	104	23% helix, 38% strand	A0A5P5Z9C8
L	Lpxtg cell wall anchor domain-containing protein	protein	120	22% helix, 38% strand	A0A5P5Z9C8

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, E, C, G, D, F, B, L
CL · Chloride ion · ion · 3 copies · chains B, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	458	0.60	0.75	51	empty
2	71	0.57	0.89	25	empty
3	230	0.48	0.74	43	empty
4	101	0.41	0.76	22	empty
5	52	0.27	0.74	18	empty

Interfaces

9 interfaces between chains.

A–E · 663 Å² buried · 18 hydrogen bonds · protein-protein
C–G · 644 Å² buried · 16 hydrogen bonds · protein-protein
B–L · 565 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 542 Å² buried · 10 hydrogen bonds · protein-protein
E–G · 159 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7CBS · Crystal structure of SpaB basal pilin from Lactobacillus rhamnosus GG · the same entry in another collection · chain B against B, 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 A0A5P5Z9C8
Elsewhere: RCSB PDB 7CBS · PDBe 7CBS · UniProt A0A5P5Z9C8

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