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Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine

Analyse Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SQL
Type: protein
Length: 1,939 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydroneopterin aldolase
UniProt: Q9SF23
Ligands: GUN
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, K, O	Dihydroneopterin aldolase	protein	120	35% helix, 32% strand	Q9SF23
B, F, G, I, N	Dihydroneopterin aldolase	protein	121	36% helix, 31% strand	Q9SF23
C, H, L	Dihydroneopterin aldolase	protein	122	33% helix, 31% strand	Q9SF23
J, M	Dihydroneopterin aldolase	protein	123	34% helix, 30% strand	Q9SF23
P	Dihydroneopterin aldolase	protein	122	35% helix, 31% strand	Q9SF23

Ligands and binding sites

GUN · Guanine · ligand · 16 copies · chains A, D, B, C, E, F, G, H, I, L, J, K, M, N, O, P

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	419	0.73	0.83	43	empty
2	381	0.73	0.84	40	empty
3	350	0.73	0.84	41	empty
4	383	0.72	0.83	41	empty
5	344	0.72	0.84	36	empty

Interfaces

35 interfaces between chains.

E–H · 1066 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1062 Å² buried · 22 hydrogen bonds · protein-protein
J–K · 1048 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1044 Å² buried · 19 hydrogen bonds · protein-protein
M–P · 1041 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1SQL · Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine · the same entry in another collection · chain K against K, 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 Q9SF23
Elsewhere: RCSB PDB 1SQL · PDBe 1SQL · UniProt Q9SF23

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