MolNFT v1 · #62143 · protein

Crystal structure of human LANCL1

3E6U · Lanc-like protein 1: “Crystal structure of human LANCL1”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.85). MolNFT v1 #62143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3E6U
Type: protein
Length: 1,618 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lanc-like protein 1
UniProt: O43813
Ligands: ZN
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lanc-like protein 1	protein	409	56% helix, 2% strand	O43813
B	Lanc-like protein 1	protein	401	57% helix, 2% strand	O43813
D	Lanc-like protein 1	protein	399	54% helix, 2% strand	O43813

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, C, B, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.85	0.87	84	empty
2	462	0.83	0.90	44	empty
3	497	0.80	0.87	94	empty
4	340	0.65	0.80	33	empty
5	315	0.64	0.80	29	empty

Interfaces

5 interfaces between chains.

A–C · 1331 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 720 Å² buried · 5 hydrogen bonds · protein-protein
C–B · 695 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 424 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 410 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3E6U · Crystal structure of Human LanCL1 · the same entry in another collection · chain A against A, TM-score 1.00
O43813 · AlphaFold monomer V2.0 prediction for glutathione S-transferase LANCL1 (O43813) · a predicted model of the same protein · chain D 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
Every structure of UniProt O43813
Elsewhere: RCSB PDB 3E6U · PDBe 3E6U · UniProt O43813

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