MolNFT v1 · #139155 · protein

Structure of P. knowlesi dbl domain capable of binding human duffy antigen

5X6N · Duffy binding protein: “Structure of P. knowlesi dbl domain capable of binding human duffy antigen”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.55). MolNFT v1 #139155 on GenesisL1: 3D structure, binding sites…

PDB: 5X6N
Type: protein
Length: 273 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Duffy binding protein
UniProt: L0SQ42
Ligands: SO4
Pockets: 6 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Duffy binding protein	protein	273	63% helix, 1% strand	L0SQ42

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A
BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

6 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	75	0.55	0.87	23	empty
2	67	0.47	0.83	13	empty
3	117	0.43	0.77	25	empty
4	50	0.41	0.82	15	empty
5	72	0.38	0.78	10	SO4

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5X6N · Structure of P. Knowlesi DBL Domain Capable of binding Human Duffy Antigen · 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 L0SQ42
Elsewhere: RCSB PDB 5X6N · PDBe 5X6N · UniProt L0SQ42

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