SMTL ID : 6rum.1

Crystal structure of GFP-LAMA-G97 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.1: 14 residues within 4Å: Chain A: N.100, D.106, F.110, S.128, I.129, I.173, Y.179, T.192, I.248, A.249, A.250, M.263, N.266 Ligands: NDP.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.110, A:F.110 Hydrogen bonds: A:S.128, A:T.192, A:I.248, A:A.249, A:A.250 Water bridges: A:N.100, A:N.100, A:T.192, A:M.263 Salt bridges: A:D.106 pi-Stacking: A:F.110

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

NDP.2: 29 residues within 4Å: Chain A: G.122, R.123, H.124, T.125, L.141, S.142, S.143, K.155, S.156, I.173, G.174, G.175, G.176, R.177, V.178, Y.179, Q.181, T.202, A.249, A.250, I.257, G.258, M.259, N.261, A.262, M.263, W.265 Ligands: TOP.1, CL.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.125 Hydrogen bonds: A:R.123, A:R.123, A:H.124, A:H.124, A:T.125, A:S.143, A:G.175, A:G.176, A:R.177, A:V.178, A:Y.179, A:Y.179, A:Q.181, A:Q.181, A:T.202, A:A.250, A:M.259, A:N.261, A:N.261 Water bridges: A:T.202 Salt bridges: A:R.123, A:H.124, A:H.124

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: E.47, W.48, G.130, R.150 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.156, V.157 Ligands: NDP.2 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Y.33, S.34, P.104 Ligand excluded by PLIP

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

PG4.6: 4 residues within 4Å: Chain A: V.94, Q.272, G.273, Q.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.275

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

PEG.7: 6 residues within 4Å: Chain A: L.183, P.184, Y.207, E.208, W.212, R.237 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.208, A:E.208, A:D.211, A:R.237, A:R.237

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-G97 a GFP enhancer nanobody with cpDHFR insertion: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GFP-LAMA-G97 a GFP enhancer nanobody with cpDHFR insertion