MolNFT v1 · #157219 · protein

NOD173 plant defensin

6MRY · NOD173 defensin: “NOD173 plant defensin”. X-ray diffraction, 2 ligands (I3C, CL), 6 pockets (best druggability 0.82). MolNFT v1 #157219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MRY
Type: protein
Length: 567 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NOD173 defensin
Ligands: I3C, CL
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	NOD173 defensin	protein	48	21% helix, 31% strand	—
B, C, D, E, F, H, I, K, L	NOD173 defensin	protein	47	21% helix, 32% strand	—

Ligands and binding sites

I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · 5 copies · chains C, J, F, H, I, G, K
CL · Chloride ion · ion · 6 copies · chains A, B, F, H, K, L
EDO · 1,2-ethanediol · additive · 11 copies · chains A, G, E, B, C, F, K, I, J, D, L
FLC · Citrate anion · additive · 6 copies · chains A, B, E, G, C, J, D, F, H, I, K
PGE · Triethylene glycol · additive · 2 copies · chains A, B, D, E, G, L
PEG · Di(hydroxyethyl)ether · additive · chains D

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	673	0.82	0.86	77	FLC, EDO
2	1142	0.79	0.81	106	EDO, PGE
3	1035	0.75	0.78	75	EDO, I3C, FLC
4	146	0.62	0.85	24	FLC
5	58	0.59	0.91	23	empty

Interfaces

31 interfaces between chains.

F–I · 603 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 593 Å² buried · 10 hydrogen bonds · protein-protein
H–K · 589 Å² buried · 11 hydrogen bonds · protein-protein
C–J · 579 Å² buried · 11 hydrogen bonds · protein-protein
B–G · 568 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

6MRY · NoD173 plant defensin · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 6MRY · PDBe 6MRY

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