SMTL ID : 6yxg.1

Cryogenic human adiponectin receptor 2 (ADIPOR2) with Tb-XO4 ligand determined by Serial Crystallography (SSX) using CrystalDirect

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: S.104, H.108, D.125, H.254, H.258 Ligands: OLA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.108, A:H.254, A:H.258

1 x OLA: OLEIC ACID(Non-covalent)

OLA.2: 19 residues within 4Å: Chain A: D.125, Y.126, I.129, A.185, F.188, M.223, L.226, Y.227, A.231, Y.234, H.254, F.257, H.258, F.260, V.261, G.264, A.265 Ligands: ZN.1, OLB.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.126, A:I.129, A:F.188, A:Y.227, A:A.231, A:Y.234, A:Y.234, A:F.257, A:F.257 Water bridges: A:H.58 Salt bridges: A:H.108, A:H.254

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

OLB.3: 10 residues within 4Å: Chain A: I.98, L.99, S.102, F.103, L.106, L.120, F.121, L.124 Ligands: OLB.8, OLB.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.99, A:F.103, A:L.106, A:F.121, A:L.124 OLB.4: 15 residues within 4Å: Chain A: S.136, F.137, W.140, G.192, L.193, G.195, I.196, T.199, I.217, L.220, M.221, A.224, Y.227, H.268 Ligands: OLA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.137, A:W.140, A:L.193, A:I.196, A:I.196, A:T.199, A:I.217, A:I.217, A:L.220, A:L.220, A:A.224, A:Y.227 OLB.5: 5 residues within 4Å: Chain A: Q.179, Y.180, G.186, L.189 Ligands: OLB.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.189 OLB.6: 9 residues within 4Å: Chain A: G.69, I.70, M.73, F.74, R.75, P.76, N.77, K.87 Ligands: OLB.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.70, A:F.74 Hydrogen bonds: A:N.77 Water bridges: A:N.77 Salt bridges: A:K.87 OLB.7: 8 residues within 4Å: Chain A: V.63, F.64, C.67, L.68, I.70, F.71, F.74, R.75 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.64, A:L.68, A:I.70, A:F.71, A:F.71, A:F.71, A:F.71, A:F.71, A:F.74 OLB.8: 9 residues within 4Å: Chain A: L.95, L.99, L.120, K.123, L.124, L.131, Q.171 Ligands: OLB.3, OLB.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.95, A:L.120, A:K.123, A:K.123, A:L.124 OLB.9: 13 residues within 4Å: Chain A: Q.85, V.88, V.89, L.92, L.95, G.96, M.134, G.135, V.138, Y.142, Y.146, L.156 Ligands: OLB.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.85, A:V.88, A:L.92, A:L.95, A:M.134, A:Y.142, A:L.156 Hydrogen bonds: A:Y.146 OLB.10: 4 residues within 4Å: Chain A: M.73, N.77, K.87 Ligands: OLB.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.87 Hydrogen bonds: A:N.77 OLB.11: 8 residues within 4Å: Chain A: L.162, V.169, W.172, Y.180, V.187, G.190, L.191 Ligands: OLB.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.162, A:V.169, A:W.172, A:Y.180, A:V.187, A:V.187 OLB.12: 10 residues within 4Å: Chain A: S.37, F.38, R.39, F.42, L.106 Chain B: N.157, H.159, N.160, G.197 Ligands: OLB.3 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.38, A:F.38, A:F.42, A:F.42, A:F.42 Hydrogen bonds: B:N.157, B:H.159, B:N.160, B:N.160, B:N.160, B:G.197 Salt bridges: B:H.159

2 x 7MT: Tb-Xo4(Non-covalent)

7MT.13: 6 residues within 4Å: Chain B: L.3, Q.5, W.108, K.171, S.172, Q.174 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:L.3, B:Q.174 Hydrogen bonds: B:S.172, B:Q.174 Salt bridges: B:K.171 7MT.14: 3 residues within 4Å: Chain B: G.42, K.43, G.229 1 PLIP interactions: 1 interactions with chain B, pi-Cation interactions: B:K.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Healey, R.D. et al., An automated platform for structural analysis of membrane proteins through serial crystallography. Cell Rep Methods (2021)

Release Date

2021-05-12

Peptides

Adiponectin receptor protein 2: A
V REGION HEAVY AND LIGHT CHAINS: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Membrane

We predict this structure to be a membrane protein.
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Adiponectin receptor protein 2

V REGION HEAVY AND LIGHT CHAINS

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