Research workbench

5NAA-bound 5-nitroanthranilate aminohydrolase

Analyse 5NAA-bound 5-nitroanthranilate aminohydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K8N
Type: protein
Length: 3,360 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-nitroanthranilic acid aminohydrolase
EC: 3.5.99.8
UniProt: D3WZ85
Ligands: 6R6
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8)	protein	420	37% helix, 22% strand	D3WZ85

Ligands and binding sites

6R6 · 5-nitroanthranilic acid · ligand · 8 copies · chains A, G, B, D, C, H, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	989	0.76	0.79	130	empty
2	1166	0.75	0.78	150	empty
3	74	0.75	0.99	30	empty
4	73	0.75	0.98	21	6R6
5	69	0.75	0.99	19	6R6

Interfaces

8 interfaces between chains.

A–G · 3607 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 3598 Å² buried · 46 hydrogen bonds · protein-protein
B–D · 3596 Å² buried · 46 hydrogen bonds · protein-protein
C–H · 3576 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 1630 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5K8N · 5NAA-bound 5-nitroanthranilate aminohydrolase · the same entry in another collection · chain H against H, TM-score 1.00
D3WZ85 · AlphaFold monomer V2.0 prediction for 5-nitroanthranilic acid aminohydrolase (D3WZ85) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 D3WZ85
Elsewhere: RCSB PDB 5K8N · PDBe 5K8N · UniProt D3WZ85

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