SMTL ID : 1zmp.7 (6 other biounits)

Crystal structure of human defensin-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-octamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: R.6, T.7, G.8 Chain G: R.13, R.32 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain A Hydrogen bonds: G:R.32, G:R.32, A:T.7, A:G.8 Water bridges: G:T.2, G:T.2, A:R.6, A:R.6, A:T.7 Salt bridges: G:R.13 SO4.2: 5 residues within 4Å: Chain B: R.6, T.7, G.8 Chain D: R.13, R.32 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:T.7, B:T.7, B:G.8, D:R.32 Water bridges: B:R.6, B:R.6, D:T.2, D:R.13 Salt bridges: D:R.13 SO4.3: 1 residues within 4Å: Chain C: R.9 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.9 SO4.5: 4 residues within 4Å: Chain D: R.9, C.10, L.16, R.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:C.10, D:L.16 Salt bridges: D:R.28 SO4.6: 4 residues within 4Å: Chain D: R.6, T.7, G.8 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.6, D:T.7, D:T.7, D:G.8 SO4.10: 1 residues within 4Å: Chain E: R.9 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.9 SO4.11: 2 residues within 4Å: Chain E: R.13, R.32 5 PLIP interactions: 5 interactions with chain E Water bridges: E:R.32, E:R.32, E:R.32 Salt bridges: E:R.13, E:R.32 SO4.13: 1 residues within 4Å: Chain F: R.9 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.9 SO4.15: 4 residues within 4Å: Chain G: R.9, C.10, L.16, R.28 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:C.10, G:L.16 Salt bridges: G:R.28 SO4.16: 4 residues within 4Å: Chain G: R.6, T.7, G.8 Ligands: GOL.19 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:R.6, G:T.7, G:T.7, G:T.7, G:G.8 SO4.20: 1 residues within 4Å: Chain H: R.9 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.9 SO4.21: 2 residues within 4Å: Chain H: R.13, R.32 4 PLIP interactions: 4 interactions with chain H Water bridges: H:R.32, H:R.32 Salt bridges: H:R.13, H:R.32

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain C: S.15 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain D: L.26, Y.27, R.28 Chain E: Y.4, R.6 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Water bridges: D:L.26 Hydrogen bonds: E:R.6, E:R.6 GOL.8: 6 residues within 4Å: Chain C: C.3, C.31 Chain D: Y.4, C.5, I.22 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.5 Water bridges: D:C.3 GOL.9: 5 residues within 4Å: Chain D: C.5, I.22, Y.27 Ligands: SO4.6, GOL.8 No protein-ligand interaction detected (PLIP) GOL.14: 1 residues within 4Å: Chain F: S.15 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain G: L.26, Y.27, R.28 Chain H: Y.4, R.6 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Water bridges: G:L.26 Hydrogen bonds: H:R.6, H:R.6 GOL.18: 6 residues within 4Å: Chain F: C.3, C.31 Chain G: Y.4, C.5, I.22 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:C.5 Water bridges: G:C.3 GOL.19: 5 residues within 4Å: Chain G: C.5, I.22, Y.27 Ligands: SO4.16, GOL.18 1 PLIP interactions: 1 interactions with chain G Water bridges: G:Y.27

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

CL.12: 1 residues within 4Å: Chain E: R.9 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain H: R.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szyk, A. et al., Crystal structures of human {alpha}-defensins HNP4, HD5, and HD6. Protein Sci. (2006)

Release Date

2006-05-30

Peptides

Defensin 5: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
A

D
C

E
B

F
A

G
C

H
B

Defensin 5

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