SMTL ID : 6qba.1

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 2T1: 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid(Non-covalent)

2T1.1: 23 residues within 4Å: Chain A: L.37, F.38, L.39, F.47, A.57, T.58, A.59, V.63, M.75, V.76, G.77, F.79, M.90, Y.92, F.98, Q.100, D.104, H.106, R.123, Y.135, F.137, F.139 Chain B: Y.25 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.37, A:A.59, A:M.75, A:Y.92, A:F.98, A:Q.100, A:Q.100, B:Y.25 Hydrogen bonds: A:L.39, A:Y.92 Water bridges: A:R.123 Salt bridges: A:R.123 Halogen bonds: A:Y.135

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 10 residues within 4Å: Chain A: R.12, V.13, K.14, E.15, V.109, D.110, R.157, E.160 Ligands: IMD.5, ZN.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.15, A:E.160 Water bridges: A:V.13 IMD.3: 5 residues within 4Å: Chain A: D.142, N.144, G.145, L.146 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142 Water bridges: A:N.144, A:L.146, A:L.146 IMD.4: 6 residues within 4Å: Chain A: Y.27, P.143, H.172, D.177 Ligands: IMD.6, ZN.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.177 pi-Stacking: A:Y.27 IMD.5: 8 residues within 4Å: Chain A: K.14, E.15, D.110, T.111, Y.116, R.157 Ligands: IMD.2, ZN.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.14, A:E.15, A:Y.116, A:R.157 pi-Cation interactions: A:R.157 IMD.6: 7 residues within 4Å: Chain A: H.172, N.173, G.174, D.177, G.178 Ligands: IMD.4, ZN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.177

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 9 residues within 4Å: Chain A: A.30, V.138, L.146, Q.151, V.154, R.155, Q.158, Y.167, L.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.151, A:Q.158 Water bridges: A:L.146, A:Q.151

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 3 residues within 4Å: Chain A: D.142, N.144 Ligands: IMD.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.142, A:D.142 ZN.9: 4 residues within 4Å: Chain A: R.12, E.15 Ligands: IMD.2, IMD.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.15, A:E.15 ZN.10: 5 residues within 4Å: Chain A: H.172, G.174, D.177 Ligands: IMD.4, IMD.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.172, A:D.177, A:D.177

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 6 residues within 4Å: Chain B: V.3, I.16, P.51, K.52, E.53, L.54 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.51, B:E.53 Water bridges: B:K.52, B:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajc, C.U. et al., A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-03

Peptides

Retinol-binding protein 4: A
DNA-binding protein 7a: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinol-binding protein 4

DNA-binding protein 7a