SMTL ID : 6qnk.1 (1 other biounit)

Antibody FAB fragment targeting Gi protein heterotrimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 8 residues within 4Å: Chain A: H.51, Y.57, H.116, L.117, Y.119 Chain B: Y.69, Y.120 Ligands: EDO.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.53, A:Y.119, A:Y.119 Water bridges: B:Y.69 PG4.2: 7 residues within 4Å: Chain A: N.55, Y.74, R.75, N.78 Chain B: Y.122, G.123 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74, A:R.75

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: R.64, Q.70, P.84, F.87, D.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.64, A:Q.70, A:D.107 EDO.4: 7 residues within 4Å: Chain A: Y.57, Y.59, R.75, H.116 Chain B: Y.120, P.126 Ligands: PG4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.59, A:Y.59 EDO.5: 5 residues within 4Å: Chain A: N.170, V.171, K.172, E.220, T.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.170, A:K.172, A:E.220, A:T.222 EDO.6: 4 residues within 4Å: Chain A: T.122, F.123 Chain B: L.64, E.65 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.123 Water bridges: B:L.64, B:L.64 EDO.8: 5 residues within 4Å: Chain A: P.144, S.146 Chain B: P.150, L.151, A.152 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.152, A:P.144 Water bridges: B:E.238, A:S.147 EDO.9: 4 residues within 4Å: Chain B: S.44, G.45, F.46, N.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.45, B:N.96 Water bridges: B:F.48 EDO.10: 5 residues within 4Å: Chain A: Y.74, S.81 Chain B: G.123, S.125 Ligands: PG4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74 Water bridges: A:S.81 EDO.11: 6 residues within 4Å: Chain A: P.69, Q.70, L.71 Chain B: D.128, F.129, W.130 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.130, B:W.130, A:L.71 Water bridges: A:L.71

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 2 residues within 4Å: Chain A: D.168, W.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.168

2 x MLT: D-MALATE(Non-covalent)

MLT.12: 6 residues within 4Å: Chain A: T.189, D.190, D.192 Chain B: V.190, H.191, T.192 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.192, B:H.191, B:T.192, B:T.192 Salt bridges: B:H.191 MLT.13: 2 residues within 4Å: Chain B: I.119, Y.121 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, C.J. et al., Cryo-EM structure of the rhodopsin-G alpha i-beta gamma complex reveals binding of the rhodopsin C-terminal tail to the G beta subunit. Elife (2019)

Release Date

2019-07-10

Peptides

FAB light chain: A
FAB heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAB light chain

FAB heavy chain

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