SMTL ID : 2ymk.1

Crystal structure of the hexameric anti-microbial peptide channel dermcidin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.38, D.42 Chain E: E.5, D.9 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Metal complexes: E:E.5, E:D.9, A:H.38, A:D.42 ZN.2: 3 residues within 4Å: Chain A: D.24, D.28 Chain E: K.20 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.28, H2O.1 ZN.3: 4 residues within 4Å: Chain B: H.38, D.42 Chain D: E.5, D.9 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:E.5, D:D.9, B:H.38, B:D.42, B:D.42 ZN.4: 2 residues within 4Å: Chain B: D.24, D.28 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.24, B:D.28, H2O.1, H2O.1 ZN.5: 4 residues within 4Å: Chain C: H.38, D.42 Chain F: E.5, D.9 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C Metal complexes: F:E.5, F:D.9, F:D.9, C:H.38, C:D.42 ZN.6: 2 residues within 4Å: Chain C: D.24, D.28 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.28, H2O.1 ZN.7: 4 residues within 4Å: Chain B: E.5, D.9 Chain D: H.38, D.42 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.38, D:D.42, B:E.5, B:D.9 ZN.8: 3 residues within 4Å: Chain B: K.20 Chain D: D.24, D.28 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.28, H2O.2 ZN.9: 4 residues within 4Å: Chain A: E.5, D.9 Chain E: H.38, D.42 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Metal complexes: A:E.5, A:D.9, E:H.38, E:D.42, E:D.42 ZN.10: 2 residues within 4Å: Chain E: D.24, D.28 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.24, E:D.28, H2O.2, H2O.2 ZN.11: 4 residues within 4Å: Chain C: E.5, D.9 Chain F: H.38, D.42 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Metal complexes: C:E.5, C:D.9, C:D.9, F:H.38, F:D.42 ZN.12: 2 residues within 4Å: Chain F: D.24, D.28 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.28, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, C. et al., Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2012-10-17

Peptides

DCD-1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

DCD-1

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