MolNFT v1 · #185584 · protein

X-ray structure of human A2ML1

7Q1Y · Alpha-2-macroglobulin-like protein 1: “X-ray structure of human A2ML1”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.75). MolNFT v1 #185584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7Q1Y
Type: protein
Length: 2,748 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-2-macroglobulin-like protein 1
UniProt: A8K2U0
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-2-macroglobulin-like protein 1	protein	1374	15% helix, 40% strand	A8K2U0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	932	0.75	0.78	76	empty
2	1025	0.74	0.77	80	empty
3	906	0.73	0.77	60	empty
4	399	0.66	0.79	64	empty
5	612	0.65	0.75	70	empty

Interfaces

1 interface between chains.

A–B · 765 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

7Q1Y · X-ray structure of human A2ML1 · the same entry in another collection · chain A against A, TM-score 1.00
A8K2U0 · AlphaFold monomer V2.0 prediction for alpha-2-macroglobulin-like protein 1 (A8K2U0) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 A8K2U0
Elsewhere: RCSB PDB 7Q1Y · PDBe 7Q1Y · UniProt A8K2U0

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