MolNFT v1 · #125273 · protein

Structure of K26-dcp

5L43 · K-26 dipeptidyl carboxypeptidase: “Structure of K26-dcp”. X-ray diffraction, 3 ligands (ZN, MG, SO4), 17 pockets (best druggability 0.88). MolNFT v1 #125273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L43
Type: protein
Length: 1,324 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: K-26 dipeptidyl carboxypeptidase
Ligands: ZN, MG, SO4
Pockets: 17 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	K-26 dipeptidyl carboxypeptidase	protein	662	59% helix, 7% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	919	0.88	0.90	100	SO4
2	648	0.85	0.89	65	SO4
3	312	0.82	0.93	55	empty
4	607	0.77	0.83	67	empty
5	367	0.73	0.84	44	empty

Interfaces

1 interface between chains.

A–B · 626 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5L43 · Structure of K26-DCP · 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 5L43 · PDBe 5L43

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