SMTL ID : 6lpk.1

A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZMA: 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol(Non-covalent)

ZMA.1: 13 residues within 4Å: Chain A: L.110, F.193, E.194, M.202, W.367, L.370, H.371, N.374, H.385, L.388, M.391, Y.392, I.395 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.110, A:W.367, A:L.388 Hydrogen bonds: A:N.374, A:N.374 Water bridges: A:K.178, A:F.193 Salt bridges: A:E.194 pi-Stacking: A:F.193, A:F.193

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.77, S.116, N.401 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.77, A:S.116

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 6 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: TRD.22, ER0.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.105 Hydrogen bonds: A:A.98 CLR.4: 9 residues within 4Å: Chain A: L.365, P.369, I.372, I.373, F.376, C.383, S.384, A.386, L.390 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.365, A:P.369, A:I.372, A:I.373, A:F.376, A:L.390 Hydrogen bonds: A:S.384 Water bridges: A:S.384 CLR.5: 6 residues within 4Å: Chain A: L.212, C.375, F.376, F.379, C.380 Ligands: MYS.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.212, A:F.376, A:F.376, A:F.376, A:F.379 Water bridges: A:F.379

1 x D12: DODECANE(Non-covalent)

D12.6: 2 residues within 4Å: Chain A: T.90 Ligands: HEX.8 No protein-ligand interaction detected (PLIP)

6 x MYS: PENTADECANE(Non-covalent)(Non-functional Binders)

MYS.7: 1 residues within 4Å: Chain A: P.387 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.387 MYS.9: 1 residues within 4Å: Ligands: ER0.23 No protein-ligand interaction detected (PLIP) MYS.14: 2 residues within 4Å: Chain A: Y.411 Ligands: 8K6.19 No protein-ligand interaction detected (PLIP) MYS.17: 1 residues within 4Å: Ligands: MYS.24 No protein-ligand interaction detected (PLIP) MYS.24: 4 residues within 4Å: Chain A: M.165, L.166 Ligands: MYS.17, 8K6.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.166 MYS.26: 2 residues within 4Å: Chain A: F.379 Ligands: CLR.5 No protein-ligand interaction detected (PLIP)

1 x HEX: HEXANE(Non-functional Binders)

HEX.8: 2 residues within 4Å: Ligands: D12.6, 8K6.10 No protein-ligand interaction detected (PLIP)

3 x 8K6: Octadecane(Non-covalent)

8K6.10: 5 residues within 4Å: Chain A: I.28, S.31, S.32, T.36 Ligands: HEX.8 No protein-ligand interaction detected (PLIP) 8K6.18: 3 residues within 4Å: Chain A: F.158 Ligands: MYS.24, TRD.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.158 8K6.19: 4 residues within 4Å: Chain A: I.358, G.361, I.408 Ligands: MYS.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.358

1 x D10: DECANE(Non-covalent)

D10.11: 2 residues within 4Å: Chain A: A.122, I.149 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.122, A:I.149, A:I.149

3 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.12: 1 residues within 4Å: Chain A: W.389 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389 OCT.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.21: 2 residues within 4Å: Chain A: Y.204, F.378 No protein-ligand interaction detected (PLIP)

1 x UND: UNDECANE(Non-covalent)

UND.15: 4 residues within 4Å: Chain A: L.47, G.48, V.50, W.54 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.47, A:V.50, A:W.54

2 x ER0: [(2~{R},3~{S})-2,3,4-tris(oxidanyl)butyl] (5~{R},9~{R},13~{R})-5,9,13,17-tetramethyloctadecanoate(Non-covalent)

ER0.16: 11 residues within 4Å: Chain A: P.27, G.30, S.31, C.366, W.389, Y.392, L.393, V.396, L.397, T.400, V.404 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.396, A:L.397, A:V.404 Hydrogen bonds: A:P.27 ER0.23: 10 residues within 4Å: Chain A: L.39, A.42, V.43, G.81, V.82, F.95, C.96, Q.188 Ligands: CLR.3, MYS.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.39, A:A.42, A:V.43 Hydrogen bonds: A:C.96, A:Q.188

4 x TRD: TRIDECANE(Non-functional Binders)(Non-covalent)

TRD.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TRD.22: 1 residues within 4Å: Ligands: CLR.3 No protein-ligand interaction detected (PLIP) TRD.25: 2 residues within 4Å: Chain A: I.78 Ligands: TRD.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.78 TRD.27: 4 residues within 4Å: Chain A: Y.68, W.154 Ligands: 8K6.18, TRD.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.68, A:W.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ihara, K. et al., Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography. Sci Rep (2020)

Release Date

2020-11-25

Peptides

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a

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