MolNFT v1 · #125360 · protein

Refolded al protein from cardiac amyloidosis

5L6Q · H5AL: “Refolded al protein from cardiac amyloidosis”. X-ray diffraction, 4 ligands (ZN, NA, CO3), 3 pockets (best druggability 0.60). MolNFT v1 #125360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L6Q
Type: protein
Length: 216 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H5AL
Ligands: ZN, NA, CO3, CL
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	H5AL	protein	108	6% helix, 52% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains A, B
NA · Sodium ion · metal · 3 copies · chains A, B
CO3 · Carbonate ion · ion · 3 copies · chains A, B
CL · Chloride ion · ion · chains B
PEG · Di(hydroxyethyl)ether · additive · chains A, B
PGE · Triethylene glycol · additive · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.60	0.80	23	PGE
2	243	0.57	0.78	22	PEG
3	126	0.43	0.76	19	NA, CO3

Interfaces

1 interface between chains.

A–B · 631 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5L6Q · Refolded AL protein from cardiac amyloidosis · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 5L6Q · PDBe 5L6Q

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