MolNFT v1 · #124216 · protein

Apo 5-nitroanthranilate aminohydrolase

5K8M · 5-nitroanthranilic acid aminohydrolase: “Apo 5-nitroanthranilate aminohydrolase”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #124216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K8M
Type: protein
Length: 1,594 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-nitroanthranilic acid aminohydrolase
EC: 3.5.99.8
UniProt: D3WZ85
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8)	protein	397	38% helix, 24% strand	D3WZ85
B	5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8)	protein	400	38% helix, 24% strand	D3WZ85
C	5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8)	protein	399	38% helix, 24% strand	D3WZ85
D	5-nitroanthranilic acid aminohydrolase (EC 3.5.99.8)	protein	398	38% helix, 23% strand	D3WZ85

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.74	0.99	36	empty
2	989	0.71	0.75	108	empty
3	462	0.69	0.80	36	empty
4	435	0.64	0.78	54	empty
5	484	0.59	0.74	59	empty

Interfaces

5 interfaces between chains.

A–D · 1823 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1811 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 532 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 297 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 11 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 43 modified (engineered).

Compared structures

5K8M · Apo 5-nitroanthranilate aminohydrolase · the same entry in another collection · chain D against D, TM-score 1.00
D3WZ85 · AlphaFold monomer V2.0 prediction for 5-nitroanthranilic acid aminohydrolase (D3WZ85) · a predicted model of the same protein · chain C 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 D3WZ85
Elsewhere: RCSB PDB 5K8M · PDBe 5K8M · UniProt D3WZ85

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