MolNFT v1 · #143624 · protein

Crystal structure of the plant defensin NAD1 complexed with phosphatidic acid

6B55 · Flower-specific defensin: “Crystal structure of the plant defensin NAD1 complexed with phosphatidic acid”. X-ray diffraction, 2 ligands (PA8, PO4), 14 pockets (best druggability 0.86). MolNFT v1 #143624 on GenesisL1: 3D structure…

PDB: 6B55
Type: protein
Length: 960 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flower-specific defensin
UniProt: Q8GTM0
Ligands: PA8, PO4
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	Flower-specific defensin	protein	48	21% helix, 31% strand	Q8GTM0

Ligands and binding sites

PA8 · 1,2-dioctanoyl-sn-glycero-3-phosphate · ligand · 14 copies · chains A, B, D, C, F, M, E, G, H, J, I, K, L, N, O, P, R, Q, T, S
PO4 · Phosphate ion · ion · 3 copies · chains B, G, J
PGE · Triethylene glycol · additive · 5 copies · chains C, E, F, B, I, K, J, L, D, M
EDO · 1,2-ethanediol · additive · 5 copies · chains G, J, L, O, Q, T

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

Pockets

14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.86	0.87	91	empty
2	581	0.80	0.86	59	PA8
3	607	0.79	0.85	53	empty
4	472	0.79	0.86	48	PGE
5	397	0.78	0.87	39	empty

Interfaces

43 interfaces between chains.

E–F · 512 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 509 Å² buried · 18 hydrogen bonds · protein-protein
S–T · 496 Å² buried · 18 hydrogen bonds · protein-protein
Q–R · 495 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 494 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 80 disulfide (disulfide).

Compared structures

6B55 · Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid · the same entry in another collection · chain K against K, 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 Q8GTM0
Elsewhere: RCSB PDB 6B55 · PDBe 6B55 · UniProt Q8GTM0

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