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Structure of legionella pneumophila histidine acid phosphatase complexed with L(+)-tartrate

Analyse Structure of legionella pneumophila histidine acid phosphatase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CDH
Type: protein
Length: 2,605 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major acid phosphatase
UniProt: Q9APF7
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Major acid phosphatase	protein	326	46% helix, 14% strand	Q9APF7
B	Major acid phosphatase	protein	325	47% helix, 14% strand	Q9APF7
C, D, F	Major acid phosphatase	protein	327	47% helix, 14% strand	Q9APF7
G	Major acid phosphatase	protein	322	46% helix, 14% strand	Q9APF7
H	Major acid phosphatase	protein	325	47% helix, 14% strand	Q9APF7

Ligands and binding sites

1PE · Pentaethylene glycol · additive · 13 copies · chains A, B, C, D, E, F, H
TLA · L(+)-tartaric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	851	0.78	0.81	101	empty
2	960	0.77	0.79	80	TLA, 1PE
3	52	0.71	0.98	25	empty
4	564	0.70	0.79	49	TLA, 1PE
5	490	0.70	0.80	45	TLA, 1PE

Interfaces

15 interfaces between chains.

A–B · 1788 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 1782 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1778 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1777 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 792 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

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 Q9APF7
Elsewhere: RCSB PDB 5CDH · PDBe 5CDH · UniProt Q9APF7

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