SMTL ID : 6shk.1

High resolution structure of the antimicrobial peptide Dermcidin from human

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K., Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel. To be published

Release Date

2019-09-25

Peptides

Dermcidin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Dermcidin

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