SMTL ID : 4xt1.1

Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 9 residues within 4Å: Chain A: I.246, I.247, L.250, P.251, L.254, T.255, S.276, A.280 Ligands: CLR.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.246, A:L.250, A:L.254, A:L.254, A:A.280 CLR.2: 7 residues within 4Å: Chain A: I.247, S.276, R.279, A.280, L.283, L.287 Ligands: CLR.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.280 Hydrogen bonds: A:S.276

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

OLC.3: 3 residues within 4Å: Chain A: P.42, V.43, F.46 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.43, A:F.46 OLC.4: 8 residues within 4Å: Chain A: G.232, V.235, R.236, I.239, A.240, L.243 Ligands: OLC.6, OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.239, A:A.240, A:L.243 Hydrogen bonds: A:R.236 OLC.5: 7 residues within 4Å: Chain A: F.54, I.57, G.58, L.297, F.301, R.307, L.310 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.54, A:I.57, A:L.297, A:F.301, A:F.301, A:L.310 Hydrogen bonds: A:R.307 OLC.6: 10 residues within 4Å: Chain A: L.209, S.213, Y.217, S.220, R.221, V.235, I.239, V.242 Ligands: OLC.4, OLC.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.209, A:I.239, A:V.242 Hydrogen bonds: A:R.221 OLC.7: 6 residues within 4Å: Chain A: L.209, S.210, Y.217, R.218, R.221 Ligands: OLC.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.217 Hydrogen bonds: A:R.218 OLC.8: 6 residues within 4Å: Chain A: V.244, L.294, L.297, L.298, R.307 Ligands: OLC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.244, A:L.294, A:L.297, A:L.298 Hydrogen bonds: A:R.307

7 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.9: 2 residues within 4Å: Chain A: S.210, Y.214 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.214 UNL.10: 2 residues within 4Å: Chain A: Q.39, V.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.39 UNL.11: 3 residues within 4Å: Chain A: S.191, I.194, I.195 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.194, A:I.195 UNL.12: 7 residues within 4Å: Chain A: Y.79, E.132, D.136, Y.139, R.147, F.155, W.159 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.136, A:Y.139, A:R.147, A:F.155, A:F.155, A:W.159, A:W.159 UNL.13: 3 residues within 4Å: Chain A: N.82, A.85, W.160 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.85, A:W.160 UNL.14: 6 residues within 4Å: Chain A: G.49, F.52, P.95, M.98, Q.99, L.102 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.52, A:P.95, A:Q.99, A:L.102 UNL.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.16: 5 residues within 4Å: Chain A: L.127, C.128, T.131, G.203, I.207 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.207 Hydrogen bonds: A:T.131, A:T.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burg, J.S. et al., Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Science (2015)

Release Date

2015-03-04

Peptides

G-protein coupled receptor homolog US28: A
Fractalkine: B
nanobody 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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G-protein coupled receptor homolog US28

Fractalkine

nanobody 7

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