SMTL ID : 5cuj.1

Crystal structure of Human Defensin-5 Y27A mutant crystal form 2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-hexamer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.21, G.24 Chain E: E.21, G.24 Chain F: E.21, G.24 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F, 2 interactions with chain E Metal complexes: A:E.21, F:E.21, F:G.24, E:E.21, E:G.24 CA.4: 6 residues within 4Å: Chain B: E.21, G.24 Chain C: E.21, G.24 Chain D: E.21, G.24 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 interactions with chain B Metal complexes: D:E.21, C:E.21, C:G.24, B:E.21, B:G.24

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: R.6, T.7, G.8 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: R.6, T.7, G.8 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain E: L.16 Ligands: CL.14 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: R.6, T.7, G.8 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: R.6, T.7, G.8 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain D: R.28 Chain F: L.16 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain E: R.6, T.7, G.8 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: L.16 Ligands: CL.6 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain F: R.6, T.7, G.8 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: L.16 Chain F: A.27 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 5 residues within 4Å: Chain C: A.1, S.17 Chain F: C.3, Y.4, C.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.1 Hydrogen bonds: C:S.17 MPD.12: 1 residues within 4Å: Chain D: R.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.32 MPD.17: 2 residues within 4Å: Chain F: A.1, R.32 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, D. et al., Human Enteric alpha-Defensin 5 Promotes Shigella Infection by Enhancing Bacterial Adhesion and Invasion. Immunity (2018)

Release Date

2016-07-27

Peptides

Defensin-5: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Defensin-5

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