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Crystal structure of 1 in complex with tafcpb

Analyse Crystal structure of 1 in complex with tafcpb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LYD
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carboxypeptidase B
EC: 3.4.17.2
UniProt: P09955
Ligands: 7B0, ZN
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carboxypeptidase B (EC 3.4.17.2)	protein	305	39% helix, 17% strand	P09955

Ligands and binding sites

7B0 · (2~{S})-6-azanyl-2-(sulfamoylamino)hexanoic acid · ligand · chains A
ZN · Zinc ion · metal · 5 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.60	0.89	22	7B0

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5LYD · Crystal structure of 1 in complex with tafCPB · the same entry in another collection · chain A against A, TM-score 1.00
P09955 · AlphaFold monomer V2.0 prediction for carboxypeptidase B (P09955) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P09955
Elsewhere: RCSB PDB 5LYD · PDBe 5LYD · UniProt P09955

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