SMTL ID : 6rul.1

Crystal structure of GFP-LAMA-F98 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.1: 12 residues within 4Å: Chain A: D.107, L.108, F.111, I.130, I.174, Y.180, T.193, I.249, A.250, A.251, M.264 Ligands: NDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.111 Hydrogen bonds: A:Y.180, A:T.193, A:I.249, A:A.250 Water bridges: A:A.250 Salt bridges: A:D.107 pi-Stacking: A:F.111

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 30 residues within 4Å: Chain A: G.123, R.124, H.125, T.126, S.129, L.142, S.143, S.144, Q.145, K.156, S.157, V.158, I.174, G.175, G.176, G.177, R.178, V.179, Y.180, Q.182, T.203, A.250, A.251, I.258, G.259, M.260, N.262, A.263, W.266 Ligands: TOP.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.126 Hydrogen bonds: A:R.124, A:H.125, A:H.125, A:T.126, A:S.129, A:S.144, A:G.176, A:G.177, A:R.178, A:V.179, A:Q.182, A:Q.182, A:T.203, A:T.203, A:A.251, A:I.258, A:M.260, A:N.262, A:N.262, A:A.263 Water bridges: A:V.158 Salt bridges: A:R.124, A:H.125, A:H.125 pi-Cation interactions: A:R.178

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

PGE.3: 7 residues within 4Å: Chain A: R.46, Y.96, E.128, S.129, E.261, N.262, W.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.46, A:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farrants, H. et al., Chemogenetic Control of Nanobodies. Nat.Methods (2020)

Release Date

2020-02-12

Peptides

GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion