- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.40 Å
- Oligo State
- homo-11-mer
- Ligands
- 33 x PLM: PALMITIC ACID(Covalent)(Non-covalent)(Non-functional Binders)
- 11 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 3 residues within 4Å:- Chain A: C.18
- Ligands: PLM.5, PLM.6
No protein-ligand interaction detected (PLIP)GOL.9: 3 residues within 4Å:- Chain B: C.18
- Ligands: PLM.7, PLM.10
No protein-ligand interaction detected (PLIP)GOL.15: 3 residues within 4Å:- Chain C: C.18
- Ligands: PLM.13, PLM.16
No protein-ligand interaction detected (PLIP)GOL.21: 3 residues within 4Å:- Chain D: C.18
- Ligands: PLM.19, PLM.22
No protein-ligand interaction detected (PLIP)GOL.27: 3 residues within 4Å:- Chain E: C.18
- Ligands: PLM.25, PLM.28
No protein-ligand interaction detected (PLIP)GOL.33: 3 residues within 4Å:- Chain F: C.18
- Ligands: PLM.31, PLM.34
No protein-ligand interaction detected (PLIP)GOL.39: 3 residues within 4Å:- Chain G: C.18
- Ligands: PLM.37, PLM.40
No protein-ligand interaction detected (PLIP)GOL.45: 3 residues within 4Å:- Chain H: C.18
- Ligands: PLM.43, PLM.46
No protein-ligand interaction detected (PLIP)GOL.51: 3 residues within 4Å:- Chain I: C.18
- Ligands: PLM.49, PLM.52
No protein-ligand interaction detected (PLIP)GOL.57: 3 residues within 4Å:- Chain J: C.18
- Ligands: PLM.55, PLM.58
No protein-ligand interaction detected (PLIP)GOL.63: 3 residues within 4Å:- Chain K: C.18
- Ligands: PLM.61, PLM.64
No protein-ligand interaction detected (PLIP)- 11 x L8Z: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)
L8Z.3: 11 residues within 4Å:- Chain A: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain B: L.70, L.74
- Ligands: L8Z.65
8 PLIP interactions:6 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:L.86, A:A.90, B:L.70, B:L.74
- Hydrogen bonds: A:G.79, A:G.80, A:T.82, A:T.82
L8Z.11: 10 residues within 4Å:- Chain B: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain C: L.70, L.74
8 PLIP interactions:6 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: B:L.86, B:A.90, C:L.70, C:L.74
- Hydrogen bonds: B:G.79, B:G.80, B:T.82, B:T.82
L8Z.17: 10 residues within 4Å:- Chain C: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain D: L.70, L.74
8 PLIP interactions:2 interactions with chain D, 6 interactions with chain C- Hydrophobic interactions: D:L.70, D:L.74, C:L.86, C:A.90
- Hydrogen bonds: C:G.79, C:G.80, C:T.82, C:T.82
L8Z.23: 10 residues within 4Å:- Chain D: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain E: L.70, L.74
8 PLIP interactions:6 interactions with chain D, 2 interactions with chain E- Hydrophobic interactions: D:L.86, D:A.90, E:L.70, E:L.74
- Hydrogen bonds: D:G.79, D:G.80, D:T.82, D:T.82
L8Z.29: 10 residues within 4Å:- Chain E: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain F: L.70, L.74
8 PLIP interactions:2 interactions with chain F, 6 interactions with chain E- Hydrophobic interactions: F:L.70, F:L.74, E:L.86, E:A.90
- Hydrogen bonds: E:G.79, E:G.80, E:T.82, E:T.82
L8Z.35: 10 residues within 4Å:- Chain F: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain G: L.70, L.74
8 PLIP interactions:6 interactions with chain F, 2 interactions with chain G- Hydrophobic interactions: F:L.86, F:A.90, G:L.70, G:L.74
- Hydrogen bonds: F:G.79, F:G.80, F:T.82, F:T.82
L8Z.41: 10 residues within 4Å:- Chain G: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain H: L.70, L.74
8 PLIP interactions:6 interactions with chain G, 2 interactions with chain H- Hydrophobic interactions: G:L.86, G:A.90, H:L.70, H:L.74
- Hydrogen bonds: G:G.79, G:G.80, G:T.82, G:T.82
L8Z.47: 10 residues within 4Å:- Chain H: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain I: L.70, L.74
8 PLIP interactions:6 interactions with chain H, 2 interactions with chain I- Hydrophobic interactions: H:L.86, H:A.90, I:L.70, I:L.74
- Hydrogen bonds: H:G.79, H:G.80, H:T.82, H:T.82
L8Z.53: 10 residues within 4Å:- Chain I: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain J: L.70, L.74
8 PLIP interactions:2 interactions with chain J, 6 interactions with chain I- Hydrophobic interactions: J:L.70, J:L.74, I:L.86, I:A.90
- Hydrogen bonds: I:G.79, I:G.80, I:T.82, I:T.82
L8Z.59: 10 residues within 4Å:- Chain J: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Chain K: L.70, T.77
8 PLIP interactions:2 interactions with chain K, 6 interactions with chain J- Hydrophobic interactions: K:L.70, K:T.77, J:L.86, J:A.90
- Hydrogen bonds: J:G.79, J:G.80, J:T.82, J:T.82
L8Z.65: 9 residues within 4Å:- Chain K: T.77, G.79, G.80, G.81, T.82, G.83, L.86, A.90
- Ligands: L8Z.3
6 PLIP interactions:6 interactions with chain K- Hydrophobic interactions: K:L.86, K:A.90
- Hydrogen bonds: K:G.79, K:G.80, K:T.82, K:T.82
- 11 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)
LPP.4: 6 residues within 4Å:- Chain A: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:A.92
- Hydrogen bonds: A:N.76
- Salt bridges: A:R.84
LPP.12: 6 residues within 4Å:- Chain B: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.92
- Hydrogen bonds: B:N.76
- Salt bridges: B:R.84
LPP.18: 6 residues within 4Å:- Chain C: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:A.92
- Hydrogen bonds: C:N.76
- Salt bridges: C:R.84
LPP.24: 6 residues within 4Å:- Chain D: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:A.92
- Hydrogen bonds: D:N.76
- Salt bridges: D:R.84
LPP.30: 6 residues within 4Å:- Chain E: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:A.92
- Hydrogen bonds: E:N.76
- Salt bridges: E:R.84
LPP.36: 6 residues within 4Å:- Chain F: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:A.92
- Hydrogen bonds: F:N.76
- Salt bridges: F:R.84
LPP.42: 6 residues within 4Å:- Chain G: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain G- Hydrophobic interactions: G:A.92
- Hydrogen bonds: G:N.76
- Salt bridges: G:R.84
LPP.48: 6 residues within 4Å:- Chain H: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain H- Hydrophobic interactions: H:A.92
- Hydrogen bonds: H:N.76
- Salt bridges: H:R.84
LPP.54: 6 residues within 4Å:- Chain I: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain I- Hydrophobic interactions: I:A.92
- Hydrogen bonds: I:N.76
- Salt bridges: I:R.84
LPP.60: 6 residues within 4Å:- Chain J: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain J- Hydrophobic interactions: J:A.92
- Hydrogen bonds: J:N.76
- Salt bridges: J:R.84
LPP.66: 6 residues within 4Å:- Chain K: A.68, N.76, R.84, S.85, T.88, A.92
3 PLIP interactions:3 interactions with chain K- Hydrophobic interactions: K:A.92
- Hydrogen bonds: K:N.76
- Salt bridges: K:R.84
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Janssens, A. et al., SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains. Nature (2023)
- Release Date
- 2022-08-03
- Peptides
- Outer membrane lipoprotein slyB: ABCDEFGHIJK
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
K - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.40 Å
- Oligo State
- homo-11-mer
- Ligands
- 33 x PLM: PALMITIC ACID(Covalent)(Non-covalent)(Non-functional Binders)
- 11 x GOL: GLYCEROL(Non-functional Binders)
- 11 x L8Z: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)
- 11 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Janssens, A. et al., SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains. Nature (2023)
- Release Date
- 2022-08-03
- Peptides
- Outer membrane lipoprotein slyB: ABCDEFGHIJK
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
K - Membrane
-
We predict this structure to be a membrane protein.