MolNFT v1 · #8706 · protein

Duck carboxypeptidase D domain II in complex with gemsa

1H8L · Carboxypeptidase GP180 residues 503-882: “Duck carboxypeptidase D domain II in complex with gemsa”. X-ray diffraction, 5 ligands (GEM, NAG, BMA), 4 pockets (best druggability 0.58). MolNFT v1 #8706 on GenesisL1: 3D structure…

PDB: 1H8L
Type: protein
Length: 380 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carboxypeptidase GP180 residues 503-882
UniProt: Q90240
Ligands: GEM, NAG, BMA, ZN, SO4
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carboxypeptidase GP180 residues 503-882	protein	380	30% helix, 25% strand	Q90240

Ligands and binding sites

GEM · (2-guanidinoethylmercapto)succinic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
BMA · beta-D-mannopyranose · sugar
ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.58	0.87	21	GEM
2	68	0.45	0.82	19	empty
3	72	0.40	0.79	20	empty
4	75	0.33	0.75	16	empty

Modifications

Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

1H8L · Duck Carboxypeptidase D Domain II in complex with GEMSA · the same entry in another collection · chain A against A, TM-score 1.00
Q90240 · AlphaFold monomer V2.0 prediction for carboxypeptidase D (Q90240) · 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 Q90240
Elsewhere: RCSB PDB 1H8L · PDBe 1H8L · UniProt Q90240

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