MolNFT v1 · #46402 · protein

Crystal structure of zebrafish ape

2O3C · Apex nuclease 1: “Crystal structure of zebrafish ape”. X-ray diffraction, 1 ligand (PB), 5 pockets (best druggability 0.77). MolNFT v1 #46402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2O3C
Type: protein
Length: 832 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apex nuclease 1
UniProt: Q7SXL6
Ligands: PB
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Apex nuclease 1	protein	276	30% helix, 25% strand	Q7SXL6
B	Apex nuclease 1	protein	280	30% helix, 25% strand	Q7SXL6

Ligands and binding sites

PB · Lead (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.77	0.81	92	PB
2	168	0.55	0.80	26	empty
3	151	0.43	0.75	26	empty
4	171	0.42	0.73	32	empty
5	81	0.31	0.73	16	empty

Interfaces

3 interfaces between chains.

B–C · 560 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 550 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 463 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2O3C · Crystal structure of zebrafish Ape · 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 Q7SXL6
Elsewhere: RCSB PDB 2O3C · PDBe 2O3C · UniProt Q7SXL6

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