SMTL ID : 7t9r.1 (3 other biounits)

Crystal structure of Crocodile defensin CpoBD13:phosphatidic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: S.1, Y.2, Y.3, S.4, T.5, N.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1, A:Y.2, A:Y.3, A:N.30

2 x PA6: (R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE(Non-covalent)

PA6.2: 6 residues within 4Å: Chain A: R.17, W.25, N.28, R.32, H.33, H.35 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.28 Salt bridges: A:R.17, A:H.33, A:H.35, A:H.35 PA6.3: 4 residues within 4Å: Chain A: S.1, Y.2, N.30, G.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.30, A:G.31

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: E.23, K.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.23, A:K.38 PO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.A. et al., Crocodile defensin (CpoBD13) antifungal activity via pH-dependent phospholipid targeting and membrane disruption. Nat Commun (2023)

Release Date

2023-01-18

Peptides

CpoBD13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CpoBD13

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