SMTL ID : 8fyn.1

MicroED structure of A2A from plasma milled lamellae

Coordinates

PDB Format

Method

ELECTRON CRYSTALLOGRAPHY 2.00 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: 18 residues within 4Å: Chain A: V.109, L.110, T.113, L.192, F.193, E.194, M.199, M.202, N.206, W.367, L.370, H.371, N.374, H.385, L.388, M.391, Y.392, I.395 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.110, A:W.367, A:L.370, A:L.388 Hydrogen bonds: A:N.374, A:N.374 Water bridges: A:E.194, A:H.371 Salt bridges: A:E.194 pi-Stacking: A:F.193, A:F.193

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 12 residues within 4Å: Chain A: L.83, F.87, F.95, A.97, A.98, G.101, C.102, F.104, I.105, Q.188 Ligands: OLC.21, OLC.25 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.83, A:F.87, A:F.87, A:F.95, A:A.97, A:A.98, A:F.104, A:I.105, A:I.105 Hydrogen bonds: A:A.98, A:Q.188 CLR.3: 13 residues within 4Å: Chain A: L.365, L.368, P.369, I.372, I.373, F.376, C.383, S.384, H.385, A.386, P.387, L.390 Ligands: OLA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.368, A:P.369, A:I.373, A:L.390 Hydrogen bonds: A:S.384 CLR.4: 11 residues within 4Å: Chain A: F.207, F.208, L.212, L.368, I.372, C.375, F.376, F.379, C.380, C.383 Ligands: OLC.24 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.207, A:F.208, A:L.212, A:L.368, A:F.376, A:F.376, A:F.376, A:F.379, A:F.379

15 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.5: 11 residues within 4Å: Chain A: L.39, V.82, P.86, I.89, T.90, T.93, F.95 Ligands: OLA.7, OLA.8, OLA.18, OLC.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.90 OLA.6: 7 residues within 4Å: Chain A: S.384, A.386, P.387, W.389, L.390, L.393 Ligands: CLR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.389, A:L.390, A:L.390 OLA.7: 6 residues within 4Å: Chain A: I.35, L.39, I.89 Ligands: OLA.5, OLA.9, OLA.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.35, A:L.39 OLA.8: 3 residues within 4Å: Ligands: OLA.5, OLA.18, OLC.21 No protein-ligand interaction detected (PLIP) OLA.9: 6 residues within 4Å: Chain A: S.32, I.35, T.36, L.39, A.40 Ligands: OLA.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.35, A:T.36 OLA.10: 10 residues within 4Å: Chain A: F.69, F.118, L.121, A.122, I.125, D.126, I.129, V.141, I.149, C.153 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.122, A:I.125, A:I.149, A:I.149 Hydrogen bonds: A:D.126 OLA.11: 3 residues within 4Å: Chain A: W.389, L.393 Ligands: OLA.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389, A:W.389 OLA.12: 6 residues within 4Å: Chain A: L.216, L.219, G.220, L.223, R.224, L.227 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.223, A:R.224 Salt bridges: A:R.224 OLA.13: 8 residues within 4Å: Chain A: V.37, I.41, L.44, T.400, V.403, V.404, F.407 Ligands: OLA.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.41, A:T.400, A:V.403, A:V.404 Hydrogen bonds: A:V.403 OLA.14: 9 residues within 4Å: Chain A: L.44, L.47, G.48, V.50, L.51, V.403, F.407, I.424, V.428 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.44, A:F.407, A:V.428 OLA.15: 15 residues within 4Å: Chain A: P.27, G.30, S.31, V.33, Y.34, V.37, I.41, L.388, W.389, Y.392, L.393, V.396, T.400 Ligands: OLA.11, OLA.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.33, A:V.37, A:Y.392, A:L.393 Hydrogen bonds: A:Y.392 OLA.16: 6 residues within 4Å: Chain A: G.148, A.151, I.152, V.155, L.156 Ligands: OLC.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.152, A:I.152, A:I.152, A:L.156 OLA.17: 10 residues within 4Å: Chain A: H.100, W.154, V.155, F.158, A.159, L.162, M.165, L.166 Ligands: OLC.22, OLC.25 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.154, A:V.155, A:F.158, A:F.158, A:L.162, A:M.165, A:L.166 OLA.18: 3 residues within 4Å: Ligands: OLA.5, OLA.7, OLA.8 No protein-ligand interaction detected (PLIP) OLA.19: 7 residues within 4Å: Chain A: I.46, V.50, C.53, W.54, W.57, I.78 Ligands: OLB.23 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.50, A:W.54, A:W.54, A:W.54, A:W.57, A:W.57, A:I.78 Hydrogen bonds: A:W.57

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.20: 8 residues within 4Å: Chain A: Y.204, F.208, L.212, V.213, L.216, F.378, F.379 Ligands: OLC.24 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.208, A:F.208, A:F.208, A:L.212, A:V.213, A:L.216 Hydrogen bonds: A:Y.204 OLC.21: 11 residues within 4Å: Chain A: V.82, L.83, P.86, F.87, T.90, F.95, C.96, I.105 Ligands: CLR.2, OLA.5, OLA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.83, A:P.86, A:F.87, A:T.90, A:F.95, A:F.95 Water bridges: A:C.96 OLC.22: 7 residues within 4Å: Chain A: V.155, L.156, A.159, M.165, L.166 Ligands: OLA.16, OLA.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.155, A:L.156, A:A.159, A:L.166 Water bridges: A:H.100 OLC.24: 5 residues within 4Å: Chain A: F.208, L.212, F.379 Ligands: CLR.4, OLC.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.208, A:L.212, A:F.379 Hydrogen bonds: A:F.379 OLC.25: 18 residues within 4Å: Chain A: Y.68, V.71, S.72, A.75, A.76, A.79, L.83, F.87, F.104, F.108, L.112, K.147, I.150, W.154, F.158 Ligands: CLR.2, OLA.17, OLB.23 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.79, A:F.104, A:F.108, A:F.108, A:L.112, A:W.154, A:W.154 Hydrogen bonds: A:S.72, A:K.147

1 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.23: 13 residues within 4Å: Chain A: C.53, V.56, W.57, Q.63, Y.68, V.71, A.75, I.78, A.79, V.82, L.83 Ligands: OLA.19, OLC.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.75, A:I.78, A:A.79, A:V.82, A:L.83

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

NA.26: 6 residues within 4Å: Chain A: A.84, F.87, I.105, A.106, F.108, V.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.105, A:F.108, A:V.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martynowycz, M.W. et al., A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Nat Commun (2023)

Release Date

2023-03-08

Peptides

Adenosine receptor A2a,Soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Adenosine receptor A2a,Soluble cytochrome b562

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