Research workbench
Crystal structure of the plant defensin NAD1 complexed with phosphatidic acid
Analyse Crystal structure of the plant defensin NAD1 complexed with phosphatidic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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.
| Volume (ų) | 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 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 509 Ų buried · 18 hydrogen bonds · protein-protein
- S–T · 496 Ų buried · 18 hydrogen bonds · protein-protein
- Q–R · 495 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 494 Ų 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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