MolNFT v1 · #15667 · protein

7,8-dihydroneopterin aldolase complexed with product from mycobacterium tuberculosis

1NBU · Probable dihydroneopterin aldolase: “7,8-dihydroneopterin aldolase complexed with product from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (PH2), 17 pockets (best druggability 0.76). MolNFT v1 #15667 on GenesisL1: 3D…

PDB: 1NBU
Type: protein
Length: 944 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable dihydroneopterin aldolase
EC: 4.1.2.25
UniProt: P0A580
Ligands: PH2
Pockets: 17 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F, G, H	Probable dihydroneopterin aldolase (EC 4.1.2.25)	protein	118	33% helix, 32% strand	P0A580
B, D	Probable dihydroneopterin aldolase (EC 4.1.2.25)	protein	118	34% helix, 31% strand	P0A580
C	Probable dihydroneopterin aldolase (EC 4.1.2.25)	protein	118	33% helix, 31% strand	P0A580

Ligands and binding sites

PH2 · 2-amino-6-hydroxymethyl-7,8-dihydro-3H-pteridin-4-one · ligand · 8 copies · chains A, D, B, C, E, H, F, G

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

Pockets

17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.76	0.97	17	empty
2	120	0.76	0.95	34	empty
3	105	0.75	0.96	26	empty
4	99	0.74	0.96	17	empty
5	664	0.62	0.73	86	empty

Interfaces

16 interfaces between chains.

F–G · 1066 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1063 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1062 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1033 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1031 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

1NBU · 7,8-Dihydroneopterin Aldolase Complexed with Product From Mycobacterium Tuberculosis · 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 P0A580
Elsewhere: RCSB PDB 1NBU · PDBe 1NBU · UniProt P0A580

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