Research workbench

Al amyloid fibril from a lambda 3 light chain in conformation B

Analyse Al amyloid fibril from a lambda 3 light chain in conformation B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z1I
Type: protein
Length: 486 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lambda 3 light chain fragment, residues 2-116
Pockets: 2 · best druggability 0.67

Structure

electron microscopy · 1 distinct chain · 0% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F, C, B, A	Lambda 3 light chain fragment, residues 2-116	protein	81	0% helix, 38% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	314	0.67	0.82	36	empty
2	187	0.42	0.74	30	empty

Interfaces

9 interfaces between chains.

B–A · 3325 Å² buried · 108 hydrogen bonds · protein-protein
D–E · 3324 Å² buried · 108 hydrogen bonds · protein-protein
D–C · 3322 Å² buried · 108 hydrogen bonds · protein-protein
C–B · 3321 Å² buried · 108 hydrogen bonds · protein-protein
E–F · 3321 Å² buried · 108 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6Z1I · AL amyloid fibril from a lambda 3 light chain in conformation B · the same entry in another collection · chain B against B, 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 6Z1I · PDBe 6Z1I

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