SMTL ID : 5cui.3 (2 other biounits)

Crystal structure of Human Defensin-5 R28A mutant.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.6, T.7 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain B: R.6, T.7, G.8 Chain C: R.6, T.7, G.8 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: E.21, I.22, S.23, G.24 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: E.21, I.22, S.23, G.24 Chain E: L.16 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: R.25, L.26 Chain E: R.9 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain D: R.6, T.7 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain E: R.6, T.7 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain F: R.6, T.7, G.8 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: L.16 Chain F: E.21, I.22, S.23, G.24 Ligand excluded by PLIP

4 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 4 residues within 4Å: Chain A: C.3, Y.4, C.5 Chain B: A.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.5, A:C.5 PG0.11: 4 residues within 4Å: Chain C: A.1 Chain D: C.3, Y.4, C.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:A.1 Hydrogen bonds: D:C.5 PG0.15: 3 residues within 4Å: Chain E: Y.4, C.5 Chain F: A.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.5 PG0.19: 5 residues within 4Å: Chain E: A.1, C.31 Chain F: Y.4, C.5, I.22 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:C.5, F:C.5 Water bridges: E:A.1

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 10 residues within 4Å: Chain B: Y.4, C.5, R.6 Chain C: Y.4, C.5, R.6, I.22 Chain D: A.1, S.17, C.31 7 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:C.5, C:R.6, C:R.6, D:S.17, B:C.5 Water bridges: A:A.1, A:A.1

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

MPD.8: 6 residues within 4Å: Chain C: R.6, T.7, G.8, L.26, Y.27, A.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.6, C:L.26, C:A.28 MPD.12: 5 residues within 4Å: Chain D: Y.4, R.6, A.11, E.14, R.32 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.4 Hydrogen bonds: D:R.6, D:E.14, D:E.14, D:R.32 MPD.16: 4 residues within 4Å: Chain E: Y.4, R.6, E.14, R.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.6

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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