SMTL ID : 3cay.1 (1 other biounit)

Crystal structure of Lipopeptide Detergent (LPD-12)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-octamer

Ligands

12 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 11 residues within 4Å: Chain A: K.9, K.12, Y.13, A.15, E.16, E.19 Chain F: X.3 Chain H: X.3, A.6, A.7, A.10 7 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: A:E.16, A:E.19, A:E.19 Water bridges: A:E.16, A:E.16, B:K.12 Hydrophobic interactions: H:A.10 LMT.2: 8 residues within 4Å: Chain A: A.7 Chain B: A.14, A.18, A.21, X.25 Chain C: K.9 Ligands: LMT.3, LMT.4 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:K.9, C:K.9 Hydrophobic interactions: A:A.7, B:A.21 LMT.3: 15 residues within 4Å: Chain A: A.11, A.14, X.25 Chain B: K.9, A.10, A.11, Y.13, A.14 Chain C: Y.13, A.17, X.25 Chain F: X.3 Ligands: LMT.2, LMT.4, LMT.5 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Y.13, C:Y.13 Hydrophobic interactions: B:A.10, B:Y.13 Water bridges: B:K.9, B:Y.13 LMT.4: 9 residues within 4Å: Chain B: Y.13, A.17, X.25 Chain C: K.9, A.10, Y.13 Ligands: LMT.2, LMT.3, LMT.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.13 LMT.5: 9 residues within 4Å: Chain C: A.14, A.17, A.18, A.21, X.25 Chain D: A.7 Ligands: LMT.3, LMT.4, LMT.7 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.14, C:A.17, C:A.21 Water bridges: C:A.21 LMT.6: 5 residues within 4Å: Chain C: X.3 Chain G: A.14, A.17, A.18 Chain H: A.11 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:A.11, G:A.14 LMT.7: 5 residues within 4Å: Chain B: X.3 Chain D: X.3, A.6, A.7 Ligands: LMT.5 No protein-ligand interaction detected (PLIP) LMT.8: 4 residues within 4Å: Chain D: K.9, A.10 Chain E: A.10, Y.13 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.10, E:Y.13, E:Y.13 LMT.9: 5 residues within 4Å: Chain F: A.6, K.9, A.10, Y.13 Ligands: LMT.11 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:A.6, F:K.9, F:A.10, F:Y.13 LMT.10: 7 residues within 4Å: Chain F: Y.13, A.17 Chain G: X.3, K.9, A.10, Y.13 Ligands: LMT.11 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:A.17 Hydrogen bonds: G:K.9 Water bridges: G:A.10 LMT.11: 10 residues within 4Å: Chain F: Y.13 Chain G: A.7, A.10, A.11, Y.13, A.14, A.17 Chain H: X.25 Ligands: LMT.9, LMT.10 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:A.11, G:Y.13, G:A.17, F:Y.13 LMT.12: 12 residues within 4Å: Chain A: X.3, A.6, A.7, A.10 Chain C: X.3 Chain H: X.3, K.9, K.12, Y.13, A.15, E.16, E.19 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:E.16, H:E.19 Water bridges: H:K.12, H:K.12 Hydrophobic interactions: A:A.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, D.N. et al., Crystal structure of a self-assembling lipopeptide detergent at 1.20 A. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-09-09

Peptides

LPD-12: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

LPD-12

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