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Geobacillus thermodenitrificans esxa crystal form I

Analyse Geobacillus thermodenitrificans esxa crystal form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZBH
Type: protein
Length: 734 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esxa
UniProt: A4IKE4
Ligands: PO4
Pockets: 7 · best druggability 0.53

Structure

x-ray diffraction · 7 distinct chains · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Esxa	protein	90	93% helix, 0% strand	A4IKE4
B	Esxa	protein	92	90% helix, 0% strand	A4IKE4
C	Esxa	protein	90	94% helix, 0% strand	A4IKE4
D	Esxa	protein	93	91% helix, 0% strand	A4IKE4
E	Esxa	protein	91	93% helix, 0% strand	A4IKE4
F, G	Esxa	protein	93	84% helix, 0% strand	A4IKE4
H	Esxa	protein	92	92% helix, 0% strand	A4IKE4

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B
ACT · Acetate ion · additive · 6 copies · chains A, B, G, C, D, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.53	0.74	31	empty
2	264	0.50	0.74	26	PO4, ACT
3	281	0.49	0.73	34	empty
4	226	0.49	0.75	33	empty
5	93	0.37	0.75	11	empty

Interfaces

7 interfaces between chains.

G–H · 1687 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1664 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1568 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1505 Å² buried · 8 hydrogen bonds · protein-protein
B–G · 606 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3ZBH · Geobacillus thermodenitrificans EsxA crystal form I · 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 A4IKE4
Elsewhere: RCSB PDB 3ZBH · PDBe 3ZBH · UniProt A4IKE4

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