Research workbench

Wild-type ampt from thermus thermophilus

Analyse Wild-type ampt from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AYI
Type: protein
Length: 1,985 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase T
EC: 3.4.11.-
UniProt: P42778
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Aminopeptidase T (EC 3.4.11.-)	protein	397	36% helix, 24% strand	P42778

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	963	0.83	0.84	88	empty
2	1150	0.79	0.80	82	ZN
3	626	0.72	0.79	43	empty
4	614	0.72	0.79	40	empty
5	1172	0.72	0.75	87	ZN

Interfaces

4 interfaces between chains.

D–E · 1644 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1635 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 561 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 526 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2AYI · Wild-type AmpT from Thermus thermophilus · the same entry in another collection · chain B against B, TM-score 1.00
P42778 · AlphaFold monomer V2.0 prediction for aminopeptidase T (P42778) · a predicted model of the same protein · chain C 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 P42778
Elsewhere: RCSB PDB 2AYI · PDBe 2AYI · UniProt P42778

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