SMTL ID : 5bk2.1 (1 other biounit)

Crystal structure of maltose binding protein in complex with a peristeric synthetic antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 14 residues within 4Å: Chain A: D.45, K.46, W.93, A.94, D.96, R.97, E.142, E.184, P.185, Y.186, F.187, W.261, W.371, R.375 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.93, A:R.97, A:R.97, A:Y.186, A:R.375 Water bridges: A:E.75, A:R.375

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

CL.2: 2 residues within 4Å: Chain A: A.194, D.195 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: K.222 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: G.65 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain B: E.164, P.165, V.166, P.183, A.184 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.164, B:V.166, B:V.166, B:A.184 GOL.4: 9 residues within 4Å: Chain B: H.38, Y.102, Y.106, Y.111, G.114, G.115 Chain C: Q.90, Y.92, I.98 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.111, C:Q.90 Water bridges: B:Y.106 GOL.5: 9 residues within 4Å: Chain B: F.182, P.183, V.185, S.193, L.194, S.195 Chain C: S.164, S.178, T.180 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.193, B:S.195, C:S.164, C:S.178, C:T.180 GOL.6: 7 residues within 4Å: Chain B: R.41, S.66, V.67, R.70, R.90, E.92, D.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.41, B:R.41, B:R.70, B:R.90 GOL.7: 9 residues within 4Å: Chain B: Y.102, K.103, W.113, G.114, G.115, D.117 Chain C: L.47, Y.50, Y.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.103, B:G.115, B:D.117, B:D.117 GOL.8: 2 residues within 4Å: Chain B: K.217, P.218 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain B: G.18, S.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.88 Water bridges: B:S.88

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

PO4.11: 4 residues within 4Å: Chain B: N.171, Q.208, T.209, I.211 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.208 PO4.13: 6 residues within 4Å: Chain C: Q.38, K.46, P.60, F.63, E.82, D.83 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.38, C:Q.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, S. et al., Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins. J. Biol. Chem. (2018)

Release Date

2018-01-17

Peptides

Maltose-binding periplasmic protein: A
sAB Heavy Chain: B
sAB Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Maltose-binding periplasmic protein

sAB Heavy Chain

sAB Light Chain

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