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Streptococcus pyogenes apo gapn

Analyse Streptococcus pyogenes apo gapn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PKJ
Type: protein
Length: 3,797 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
UniProt: A0A7G1J7Q1
Ligands: SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	protein	474	43% helix, 24% strand	A0A7G1J7Q1
C, D, E, G, H	Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	protein	475	43% helix, 24% strand	A0A7G1J7Q1

Ligands and binding sites

SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, F, D, E, G, H
GOL · Glycerol · additive · 25 copies · chains A, B, D, C, F, E, G, H
BME · Beta-mercaptoethanol · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.86	0.87	113	GOL
2	973	0.84	0.86	83	GOL
3	771	0.84	0.87	77	SO4
4	756	0.83	0.87	74	GOL
5	357	0.75	0.86	43	empty

Interfaces

17 interfaces between chains.

G–H · 2456 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2450 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2449 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 2436 Å² buried · 29 hydrogen bonds · protein-protein
E–H · 1193 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (additive adduct).

Compared structures

7PKJ · Streptococcus pyogenes apo GapN · 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 A0A7G1J7Q1
Elsewhere: RCSB PDB 7PKJ · PDBe 7PKJ · UniProt A0A7G1J7Q1

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