SMTL ID : 6yxf.1

Cryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 ligand determined by Serial Crystallography (SSX) using CrystalDirect

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: S.104, H.108, 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: 18 residues within 4Å: Chain A: D.125, Y.126, I.129, L.132, R.184, A.185, F.188, L.189, M.223, Y.227, A.231, Y.234, H.254, F.257, F.260, G.264 Ligands: ZN.1, OLB.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.126, A:Y.126, A:I.129, A:L.132, A:R.184, A:F.188, A:Y.227, A:Y.227, A:F.257 Salt bridges: A:H.108, A:H.254

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

OLB.3: 15 residues within 4Å: Chain A: S.136, F.137, G.192, L.193, G.195, I.196, T.199, F.208, I.217, L.220, M.221, M.223, Y.227, H.268 Ligands: OLA.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.137, A:I.196, A:T.199, A:I.217, A:L.220, A:L.220, A:M.223 OLB.4: 9 residues within 4Å: Chain A: G.69, I.70, M.73, F.74, R.75, P.76, N.77, K.87 Ligands: OLB.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.70, A:F.74, A:F.74 Hydrogen bonds: A:N.77 Salt bridges: A:K.87 OLB.5: 8 residues within 4Å: Chain A: V.63, F.64, C.67, L.68, I.70, F.71, F.74, R.75 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.68, A:I.70, A:F.71, A:F.71, A:F.71 OLB.6: 11 residues within 4Å: Chain A: Q.85, V.89, L.92, L.95, L.131, M.134, V.138, Y.142, Y.146, C.152, L.156 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.85, A:V.89, A:L.92, A:L.95, A:M.134, A:V.138 Hydrogen bonds: A:Q.85 OLB.7: 4 residues within 4Å: Chain A: M.73, N.77, L.92 Ligands: OLB.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.92 Hydrogen bonds: A:N.77 OLB.12: 11 residues within 4Å: Chain A: S.37, F.38, R.39, F.42, S.102, L.106 Chain B: N.149, H.151, N.152, S.188, G.189 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.42, A:F.42, A:F.42, A:L.106, A:L.106 Hydrogen bonds: A:F.38, A:R.39, B:N.149, B:N.152, B:G.189 Salt bridges: B:H.151

3 x GD: GADOLINIUM ATOM(Non-functional Binders)(Non-covalent)

GD.8: 2 residues within 4Å: Ligands: DO3.10, DO3.14 No protein-ligand interaction detected (PLIP) GD.9: 2 residues within 4Å: Chain A: E.115 Ligands: DO3.11 No protein-ligand interaction detected (PLIP) GD.13: 2 residues within 4Å: Ligands: DO3.10, DO3.14 No protein-ligand interaction detected (PLIP)

3 x DO3: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID(Non-covalent)

DO3.10: 9 residues within 4Å: Chain A: R.10, V.11, H.29, I.48, I.249 Chain B: N.54 Ligands: GD.8, GD.13, DO3.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.11 Salt bridges: A:H.29 DO3.11: 3 residues within 4Å: Chain A: E.115, R.119 Ligands: GD.9 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:E.115, A:E.115, A:E.115, A:E.115 DO3.14: 6 residues within 4Å: Chain B: N.54, S.55, K.74 Ligands: GD.8, DO3.10, GD.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.54, B:N.54 Salt bridges: A:R.10

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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