MolNFT v1 · #145929 · protein

Structure of ulvan lyase from nonlaben ulvanivorans- NLR48

6D2C: “Structure of ulvan lyase from nonlaben ulvanivorans- NLR48”. X-ray diffraction, 2 ligands (CA, PO4), 2 pockets (best druggability 0.77). MolNFT v1 #145929 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D2C
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ulvan lyase
UniProt: A0A084JZF2
Ligands: CA, PO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ulvan lyase	protein	260	5% helix, 49% strand	A0A084JZF2

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1096	0.77	0.79	93	PO4, EDO
2	82	0.55	0.86	20	empty

Interfaces

1 interface between chains.

A–B · 649 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 disulfide (engineered, disulfide).

Compared structures

6D2C · Structure of Ulvan lyase from Nonlaben Ulvanivorans- NLR48 · 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
Every structure of UniProt A0A084JZF2
Elsewhere: RCSB PDB 6D2C · PDBe 6D2C · UniProt A0A084JZF2

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