SMTL ID : 1zmi.3 (5 other biounits)

Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-octamer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: C.3, Y.20, W.25 Chain B: F.27 Chain G: I.5 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.3 Water bridges: A:C.3, A:C.3 GOL.2: 7 residues within 4Å: Chain A: P.6, A.7, I.9 Chain E: I.5, R.23, W.25 Ligands: GOL.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:A.7, A:A.7, E:R.23, E:R.23 Water bridges: E:I.5, E:I.5 GOL.6: 5 residues within 4Å: Chain A: C.1, F.27 Chain B: Y.2, C.3, Y.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.3, B:C.3, B:Y.20 GOL.7: 7 residues within 4Å: Chain B: R.4, I.5, P.6, R.14, L.24, W.25, A.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.4, B:R.14, B:R.14, B:A.26 GOL.8: 6 residues within 4Å: Chain C: C.3, Y.20, W.25 Chain D: F.27 Chain E: I.5 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.3 Water bridges: C:C.3, C:C.3 GOL.9: 7 residues within 4Å: Chain C: P.6, A.7, I.9 Chain G: I.5, R.23, W.25 Ligands: GOL.1 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain G Hydrogen bonds: C:A.7, C:A.7, G:R.23, G:R.23 Water bridges: G:I.5, G:I.5 GOL.13: 5 residues within 4Å: Chain C: C.1, F.27 Chain D: Y.2, C.3, Y.20 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.3, D:C.3 GOL.14: 7 residues within 4Å: Chain D: R.4, I.5, P.6, R.14, L.24, W.25, A.26 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.4, D:R.14, D:R.14, D:A.26

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

SO4.3: 4 residues within 4Å: Chain B: R.13, C.29 Chain G: A.7, R.14 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Water bridges: G:R.14, G:R.14 Salt bridges: G:R.14, B:R.13 Hydrogen bonds: B:C.29 SO4.4: 4 residues within 4Å: Chain B: G.11 Chain G: R.14, A.16, T.17 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B Salt bridges: G:R.14 Water bridges: B:G.11 SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.10: 4 residues within 4Å: Chain D: R.13, C.29 Chain E: A.7, R.14 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:C.29 Salt bridges: D:R.13, E:R.14 Water bridges: E:R.14, E:R.14 SO4.11: 4 residues within 4Å: Chain D: G.11 Chain E: R.14, A.16, T.17 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Salt bridges: E:R.14 Water bridges: D:G.11 SO4.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, C. et al., Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. J.Biol.Chem. (2005)

Release Date

2005-08-16

Peptides

Neutrophil defensin 2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
C

F
D

G
C

H
D

Neutrophil defensin 2

Related Entries With Identical Sequence