MolNFT v1 · #115893 · protein

Crystal structure of FYCO1 lir in complex with LC3A

5CX3 · Microtubule-associated proteins 1A/1B light chain 3A: “Crystal structure of FYCO1 lir in complex with LC3A”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #115893 on GenesisL1: 3D structure, binding sites and…

PDB: 5CX3
Type: protein
Length: 553 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microtubule-associated proteins 1A/1B light chain 3A; Fyve and coiled-coil…
UniProt: Q9H492, Q9BQS8
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 7 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Microtubule-associated proteins 1A/1B light chain 3A	protein	119	35% helix, 25% strand	Q9H492
B	Microtubule-associated proteins 1A/1B light chain 3A	protein	118	35% helix, 24% strand	Q9H492
D	Microtubule-associated proteins 1A/1B light chain 3A	protein	117	35% helix, 24% strand	Q9H492
E	Fyve and coiled-coil domain-containing protein 1	protein	20	25% helix, 35% strand	Q9BQS8
F	Fyve and coiled-coil domain-containing protein 1	protein	25	24% helix, 8% strand	Q9BQS8
G	Fyve and coiled-coil domain-containing protein 1	protein	19	21% helix, 11% strand	Q9BQS8
H	Fyve and coiled-coil domain-containing protein 1	protein	16	25% helix, 13% strand	Q9BQS8

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.63	0.80	28	empty
2	235	0.54	0.77	37	empty
3	138	0.51	0.80	26	empty
4	155	0.45	0.76	28	empty
5	152	0.44	0.75	31	empty

Interfaces

8 interfaces between chains.

A–E · 951 Å² buried · 17 hydrogen bonds · protein-protein
B–F · 930 Å² buried · 18 hydrogen bonds · protein-protein
C–G · 910 Å² buried · 18 hydrogen bonds · protein-protein
D–H · 779 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 645 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5CX3 · Crystal structure of FYCO1 LIR in complex with LC3A · the same entry in another collection · chain H against H, TM-score 1.00
Q9H492 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain B against A, TM-score 0.96
Q9BQS8 · AlphaFold monomer V2.0 prediction for fyve and coiled-coil domain- containing protein 1… · a predicted model of the same protein · chain H against A, TM-score 0.38

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 Q9H492
Every structure of UniProt Q9BQS8
Elsewhere: RCSB PDB 5CX3 · PDBe 5CX3 · UniProt Q9H492 · UniProt Q9BQS8

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