SMTL ID : 5wb2.1

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 8 residues within 4Å: Chain A: I.246, P.250, L.253, T.254, V.257, F.272, A.279 Ligands: CLR.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.246, A:P.250, A:L.253, A:L.253, A:V.257, A:V.257, A:A.279 CLR.2: 6 residues within 4Å: Chain A: S.275, R.278, A.279, L.282, T.283 Ligands: CLR.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.279, A:L.282, A:T.283

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

OLC.3: 8 residues within 4Å: Chain A: F.53, R.232, R.235, V.236, A.239, L.293, L.297, V.301 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.53, A:A.239, A:L.293, A:L.297 Hydrogen bonds: A:R.235 OLC.4: 7 residues within 4Å: Chain A: R.146, F.157, F.161, E.198, L.201, I.206 Ligands: OLC.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.157, A:F.161, A:E.198, A:L.201 Hydrogen bonds: A:R.146 OLC.5: 7 residues within 4Å: Chain A: I.62, I.80, A.84, L.87, L.88, L.113, C.117 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.62, A:A.84, A:L.87, A:L.88, A:L.113, A:L.113 OLC.6: 6 residues within 4Å: Chain A: F.123, T.130, W.158, G.202, I.206 Ligands: OLC.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.123, A:T.130, A:W.158, A:I.206

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain B: V.21, H.64 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.64

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 11 residues within 4Å: Chain A: W.96, T.115, V.173, C.180, T.182, Y.184 Chain B: L.1, L.2, P.3, H.4, N.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.4, B:N.6, A:T.182, A:T.182, A:T.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, T.F. et al., Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy. Elife (2018)

Release Date

2018-06-13

Peptides

Envelope protein US28, nanobody 7 fusion protein: A
CX3CL1 protein: B
nanobody B1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Envelope protein US28, nanobody 7 fusion protein

CX3CL1 protein

nanobody B1