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Crystal structure of MAPE1

Analyse Crystal structure of MAPE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JGF
Type: protein
Length: 1,842 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar aminopeptidase 1
EC: 3.4.11.22
UniProt: P14904
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Vacuolar aminopeptidase 1 (EC 3.4.11.22)	protein	460	32% helix, 23% strand	P14904
D	Vacuolar aminopeptidase 1 (EC 3.4.11.22)	protein	462	32% helix, 24% strand	P14904

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

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.83	0.95	37	empty
2	316	0.64	0.80	57	empty
3	67	0.62	0.92	24	empty
4	95	0.59	0.87	30	empty
5	147	0.55	0.81	43	empty

Interfaces

3 interfaces between chains.

C–D · 3280 Å² buried · 59 hydrogen bonds · protein-protein
A–B · 3242 Å² buried · 58 hydrogen bonds · protein-protein
B–D · 1758 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5JGF · Crystal structure of mApe1 · the same entry in another collection · chain D against D, TM-score 1.00
P14904 · AlphaFold monomer V2.0 prediction for vacuolar aminopeptidase 1 (P14904) · a predicted model of the same protein · chain B 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 P14904
Elsewhere: RCSB PDB 5JGF · PDBe 5JGF · UniProt P14904

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