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Crystal structure of a yada-like head domain of the trimeric autotransporter adhesin boaa from burkholderia pseudomallei solved by iodide ion sad phasing

Analyse Crystal structure of a yada-like head domain of the trimeric autotransporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S6L
Type: protein
Length: 777 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HEP_HAG family
UniProt: Q3JFX2
Ligands: ZN, IOD, CL
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HEP_HAG family	protein	155	5% helix, 33% strand	Q3JFX2
B	HEP_HAG family	protein	153	3% helix, 34% strand	Q3JFX2
D	HEP_HAG family	protein	158	7% helix, 28% strand	Q3JFX2
E	HEP_HAG family	protein	156	6% helix, 28% strand	Q3JFX2

Ligands and binding sites

ZN · Zinc ion · metal · 17 copies · chains A, E, B, D, C
IOD · Iodide ion · ion · 53 copies · chains A, B, C, E, D
CL · Chloride ion · ion · 25 copies · chains A, C, B, D, E

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

Pockets

3 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	569	0.69	0.79	83	IOD
2	534	0.67	0.78	82	IOD, CL
3	52	0.28	0.75	17	IOD

Interfaces

5 interfaces between chains.

A–C · 2036 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2035 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1993 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 498 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 465 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3S6L · Crystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA… · the same entry in another collection · chain A against A, 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 Q3JFX2
Elsewhere: RCSB PDB 3S6L · PDBe 3S6L · UniProt Q3JFX2

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