SMTL ID : 5m13.1

Synthetic nanobody in complex with MBP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: T.196, V.199, D.200, K.203, V.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.196, A:D.200 EDO.2: 5 residues within 4Å: Chain A: D.167, A.189, G.190, A.193, K.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167, A:K.254 Water bridges: A:K.254 EDO.3: 7 residues within 4Å: Chain B: R.39, Q.40, A.41, K.44, E.45, E.47 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.41, B:E.45 Water bridges: B:R.39, B:E.90 EDO.4: 6 residues within 4Å: Chain B: R.39, E.47, G.48, A.62, S.64 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.39, B:R.39, B:S.64 Water bridges: B:S.64, B:S.64 EDO.5: 4 residues within 4Å: Chain B: W.111, F.112, Y.113, R.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.112 Water bridges: B:R.114 EDO.6: 5 residues within 4Å: Chain A: Y.93, M.324, Q.328 Chain B: G.11, S.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.12 EDO.7: 4 residues within 4Å: Chain B: R.46, Q.110, W.111, W.116 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.46, B:Q.110 Water bridges: B:Q.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmermann, I. et al., Synthetic single domain antibodies for the conformational trapping of membrane proteins. Elife (2018)

Release Date

2017-11-15

Peptides

Maltose-binding periplasmic protein: A
synthetic Nanobody L2_C06 (a-MBP#2): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Maltose-binding periplasmic protein

synthetic Nanobody L2_C06 (a-MBP#2)

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