MolNFT v1 · #27302 · protein

Crystal structure of an archaeal aminopeptidase

1XFO · Frv operon protein frvx: “Crystal structure of an archaeal aminopeptidase”. X-ray diffraction, 1 ligand (ZN), 19 pockets (best druggability 0.70). MolNFT v1 #27302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XFO
Type: protein
Length: 1,357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Frv operon protein frvx
UniProt: O59196
Ligands: ZN
Pockets: 19 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Frv operon protein frvx	protein	346	29% helix, 30% strand	O59196
B, C, D	Frv operon protein frvx	protein	337	31% helix, 31% strand	O59196

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

19 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	73	0.70	0.95	17	empty
2	261	0.65	0.82	45	empty
3	54	0.63	0.94	16	empty
4	468	0.61	0.75	32	empty
5	299	0.58	0.77	49	empty

Interfaces

4 interfaces between chains.

A–D · 2030 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 1276 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1245 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 1230 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1XFO · Crystal Structure of an archaeal aminopeptidase · the same entry in another collection · chain A against A, TM-score 1.00
O59196 · AlphaFold monomer V2.0 prediction for tetrahedral aminopeptidase (O59196) · a predicted model of the same protein · chain B 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 O59196
Elsewhere: RCSB PDB 1XFO · PDBe 1XFO · UniProt O59196

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