SMTL ID : 1zmp.6 (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: 1 residues within 4Å: Chain A: R.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.9 SO4.3: 5 residues within 4Å: Chain B: R.9, C.10, L.16, R.28 Chain G: A.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:C.10, B:L.16, G:A.1 Salt bridges: B:R.28 Water bridges: G:T.2 SO4.4: 4 residues within 4Å: Chain B: R.6, T.7, G.8 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.6, B:T.7, B:T.7, B:G.8 SO4.8: 1 residues within 4Å: Chain C: R.9 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.9 SO4.10: 5 residues within 4Å: Chain D: R.9, C.10, L.16, R.28 Chain E: A.1 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:A.1, E:A.1, D:C.10, D:L.16 Water bridges: E:T.2 Salt bridges: D:R.28 SO4.11: 4 residues within 4Å: Chain D: R.6, T.7, G.8 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.6, D:T.7, D:T.7, D:T.7, D:G.8 SO4.15: 1 residues within 4Å: Chain E: R.9 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.9 SO4.16: 2 residues within 4Å: Chain E: R.13, R.32 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.32 Salt bridges: E:R.13, E:R.32 SO4.18: 5 residues within 4Å: Chain D: R.13, R.32 Chain F: R.6, T.7, G.8 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:R.32, D:R.32, F:T.7, F:G.8 Water bridges: D:T.2, D:T.2, F:R.6, F:R.6, F:T.7 Salt bridges: D:R.13 SO4.19: 1 residues within 4Å: Chain G: R.9 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.9 SO4.20: 2 residues within 4Å: Chain G: R.13, R.32 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:R.13, G:R.32 SO4.22: 5 residues within 4Å: Chain B: R.13, R.32 Chain H: R.6, T.7, G.8 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain H Hydrogen bonds: B:R.32, H:T.7, H:T.7, H:G.8 Water bridges: B:T.2, B:R.13, H:R.6, H:R.6 Salt bridges: B:R.13

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: S.15 No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain B: L.26, Y.27, R.28 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.26 GOL.6: 6 residues within 4Å: Chain A: C.3, C.31 Chain B: Y.4, C.5, I.22 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.5 Water bridges: B:C.3 GOL.7: 5 residues within 4Å: Chain B: C.5, I.22, Y.27 Ligands: SO4.4, GOL.6 No protein-ligand interaction detected (PLIP) GOL.9: 1 residues within 4Å: Chain C: S.15 No protein-ligand interaction detected (PLIP) GOL.12: 3 residues within 4Å: Chain D: L.26, Y.27, R.28 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.26 GOL.13: 6 residues within 4Å: Chain C: C.3, C.31 Chain D: Y.4, C.5, I.22 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.5 Water bridges: D:C.3 GOL.14: 5 residues within 4Å: Chain D: C.5, I.22, Y.27 Ligands: SO4.11, GOL.13 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.27

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

CL.17: 1 residues within 4Å: Chain E: R.9 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain G: 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
A

B
C

C
A

D
C

E
B

F
D

G
B

H
D

Defensin 5

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