SMTL ID : 7sai.1

Crystal Structure of Lag30 Nanobody bound to eGFP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

hetero-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: P.74, D.75, H.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.75, A:D.75, A:D.75, A:H.76, A:H.76 GOL.2: 4 residues within 4Å: Chain A: K.106, T.107, R.108, E.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.106, A:R.108 GOL.6: 10 residues within 4Å: Chain B: A.54, M.55, G.56, F.68, T.118, A.119, R.120, L.129, S.134, F.135 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.118, B:S.134 Water bridges: B:T.118, B:T.118 GOL.7: 4 residues within 4Å: Chain B: R.40, S.92, R.93, D.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.40, B:S.92 Water bridges: B:D.94 GOL.8: 3 residues within 4Å: Chain B: G.31, Q.143, T.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.31, B:T.145

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 5 residues within 4Å: Chain A: I.187, G.188, D.189 Chain B: R.122, D.136 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.136 Salt bridges: A:D.189

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: K.130, E.131, D.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.131, A:D.132, A:D.132 PO4.5: 5 residues within 4Å: Chain A: P.57, W.58, P.59, H.138, Y.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.58 Water bridges: A:K.53 Salt bridges: A:K.53 PO4.9: 3 residues within 4Å: Chain B: T.75, V.76, R.93 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.93, B:R.93 Salt bridges: B:R.93 PO4.10: 3 residues within 4Å: Chain B: R.66, F.135, K.138 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.66, B:K.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cong, A.T.Q. et al., High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices. Protein Sci. (2022)

Release Date

2022-09-14

Peptides

Green fluorescent protein: A
LAG30 Nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Green fluorescent protein

LAG30 Nanobody

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