SMTL ID : 1zmp.5 (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.9 Chain D: V.19 Chain G: R.6, T.7, G.8 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain G Salt bridges: A:R.9, G:R.6 Hydrogen bonds: G:T.7, G:G.8, G:G.8 Water bridges: G:R.6, G:R.6 SO4.2: 2 residues within 4Å: Chain A: R.13, R.32 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.32 Salt bridges: A:R.13, A:R.32 SO4.4: 5 residues within 4Å: Chain B: R.9 Chain C: V.19 Chain E: R.6, T.7, G.8 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain E Salt bridges: B:R.9, E:R.6 Hydrogen bonds: E:T.7, E:G.8, E:G.8 Water bridges: E:R.6, E:R.6 SO4.5: 2 residues within 4Å: Chain B: R.13, R.32 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.13, B:R.32 SO4.7: 5 residues within 4Å: Chain C: R.6, T.7, G.8 Chain H: R.13, R.32 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain H Hydrogen bonds: C:T.7, C:G.8, H:R.32, H:R.32 Water bridges: C:R.6, C:R.6, C:T.7, H:T.2, H:T.2 Salt bridges: H:R.13 SO4.8: 5 residues within 4Å: Chain D: R.6, T.7, G.8 Chain F: R.13, R.32 9 PLIP interactions: 4 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:R.32, D:T.7, D:T.7, D:G.8 Water bridges: F:T.2, F:R.13, D:R.6, D:R.6 Salt bridges: F:R.13 SO4.9: 4 residues within 4Å: Chain B: R.6, T.7, G.8 Chain E: R.9 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:T.7, B:T.7, B:G.8 Water bridges: B:R.6, B:T.7 Salt bridges: B:R.6, E:R.9 SO4.11: 4 residues within 4Å: Chain F: R.9, C.10, L.16, R.28 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:C.10, F:L.16 Salt bridges: F:R.28 SO4.12: 4 residues within 4Å: Chain F: R.6, T.7, G.8 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.6, F:T.7, F:T.7, F:G.8 SO4.16: 4 residues within 4Å: Chain A: R.6, T.7, G.8 Chain G: R.9 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:T.7, A:T.7, A:G.8 Water bridges: A:R.6 Salt bridges: A:R.6, G:R.9 SO4.18: 4 residues within 4Å: Chain H: R.9, C.10, L.16, R.28 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:C.10, H:L.16 Salt bridges: H:R.28 SO4.19: 4 residues within 4Å: Chain H: R.6, T.7, G.8 Ligands: GOL.22 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:R.6, H:T.7, H:T.7, H:T.7, H:G.8

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

CL.3: 2 residues within 4Å: Chain A: R.9 Chain G: R.9 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.9 Chain E: R.9 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain B: R.13 Chain E: S.15 2 PLIP interactions: 2 interactions with chain E Water bridges: E:L.16, E:L.16 GOL.13: 3 residues within 4Å: Chain F: L.26, Y.27, R.28 1 PLIP interactions: 1 interactions with chain F Water bridges: F:L.26 GOL.14: 6 residues within 4Å: Chain E: C.3, C.31 Chain F: Y.4, C.5, I.22 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:C.5 Water bridges: F:C.3 GOL.15: 5 residues within 4Å: Chain F: C.5, I.22, Y.27 Ligands: SO4.12, GOL.14 No protein-ligand interaction detected (PLIP) GOL.17: 2 residues within 4Å: Chain A: R.13 Chain G: S.15 2 PLIP interactions: 2 interactions with chain G Water bridges: G:L.16, G:L.16 GOL.20: 3 residues within 4Å: Chain H: L.26, Y.27, R.28 1 PLIP interactions: 1 interactions with chain H Water bridges: H:L.26 GOL.21: 6 residues within 4Å: Chain G: C.3, C.31 Chain H: Y.4, C.5, I.22 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:C.5 Water bridges: H:C.3 GOL.22: 5 residues within 4Å: Chain H: C.5, I.22, Y.27 Ligands: SO4.19, GOL.21 1 PLIP interactions: 1 interactions with chain H Water bridges: H:Y.27

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
B

B
B

C
D

D
D

E
A

F
C

G
A

H
C

Defensin 5

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