MolNFT v1 · #170921 · protein

Inducible lysine decarboxylase ldci decamer, pH 7.0

6YN5: “Inducible lysine decarboxylase ldci decamer, pH 7.0”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #170921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YN5
Type: protein
Length: 7,110 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inducible lysine decarboxylase
EC: 4.1.1.18
UniProt: P0A9H3
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Inducible lysine decarboxylase (EC 4.1.1.18)	protein	711	42% helix, 17% strand	P0A9H3

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	1169	0.85	0.86	116	empty
2	1108	0.85	0.86	110	empty
3	1021	0.85	0.86	114	empty
4	1127	0.85	0.86	118	empty
5	916	0.83	0.85	78	empty

Interfaces

20 interfaces between chains.

E–I · 5185 Å² buried · 58 hydrogen bonds · protein-protein
D–J · 5182 Å² buried · 56 hydrogen bonds · protein-protein
B–G · 5164 Å² buried · 51 hydrogen bonds · protein-protein
C–F · 5161 Å² buried · 53 hydrogen bonds · protein-protein
A–H · 5142 Å² buried · 50 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (cofactor).

Compared structures

6YN5 · Inducible lysine decarboxylase LdcI decamer, pH 7.0 · the same entry in another collection · chain J against J, TM-score 1.00
P0A9H3 · AlphaFold monomer V2.0 prediction for inducible lysine decarboxylase (P0A9H3) · a predicted model of the same protein · 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
Every structure of UniProt P0A9H3
Elsewhere: RCSB PDB 6YN5 · PDBe 6YN5 · UniProt P0A9H3

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