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Crystal structure of ampd holoenzyme

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

PDB: 2Y2D
Type: protein
Length: 537 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampd
EC: 3.5.1.28
UniProt: P82974
Ligands: ZN
Pockets: 5 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampd (EC 3.5.1.28)	protein	179	22% helix, 22% strand	P82974

Ligands and binding sites

ZN · Zinc 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.55	0.83	34	empty
2	205	0.53	0.78	28	empty
3	209	0.51	0.76	26	empty
4	181	0.51	0.77	29	empty
5	110	0.42	0.77	21	empty

Interfaces

2 interfaces between chains.

A–B · 267 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 174 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2Y2D · crystal structure of AmpD holoenzyme · the same entry in another collection · chain A against A, TM-score 1.00
P82974 · AlphaFold monomer V2.0 prediction for 1,6-anhydro-N-acetylmuramyl-L- alanine amidase ampd… · 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 P82974
Elsewhere: RCSB PDB 2Y2D · PDBe 2Y2D · UniProt P82974

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