MolNFT v1 · #85977 · protein

Crystal structure of the catalytic domain of beta-agarase D from zobellia galactanivorans

4ASM: “Crystal structure of the catalytic domain of beta-agarase D from zobellia galactanivorans”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.63). MolNFT v1 #85977 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4ASM
Type: protein
Length: 357 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-agarase D
EC: 3.2.1.81
UniProt: D7GXG4
Ligands: CA
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Beta-agarase D (EC 3.2.1.81)	protein	357	8% helix, 40% strand	D7GXG4

Ligands and binding sites

CA · Calcium ion · metal · chains B
IMD · Imidazole · additive · chains B
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

2 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	397	0.63	0.77	40	IMD, PEG
2	57	0.33	0.77	13	empty

Compared structures

4ASM · Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans · the same entry in another collection · chain B against B, TM-score 1.00
D7GXG4 · AlphaFold monomer V2.0 prediction for beta-agarase D (D7GXG4) · a predicted model of the same protein · chain B 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 D7GXG4
Elsewhere: RCSB PDB 4ASM · PDBe 4ASM · UniProt D7GXG4

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