SMTL ID : 4ej1.2 (1 other biounit)

Binding of Nb113 camelid antibody fragment with the binary DHFR:folate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-oligomer

Ligands

1 x FOL: FOLIC ACID(Non-covalent)

FOL.1: 16 residues within 4Å: Chain A: I.5, A.6, A.7, E.17, D.27, L.28, W.30, F.31, K.32, T.46, I.50, L.54, R.57, I.94, Y.100, T.113 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.17, A:F.31, A:F.31, A:I.50 Hydrogen bonds: A:Y.100, A:T.113, A:T.113 Water bridges: A:A.6, A:A.7, A:D.27, A:R.52 Salt bridges: A:D.27, A:R.57

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

PO4.2: 9 residues within 4Å: Chain A: M.16, G.43, R.44, H.45, T.46, G.95, G.96, R.98, V.99 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.43, A:G.43, A:H.45, A:T.46, A:G.96 Water bridges: A:R.44, A:G.97 Salt bridges: A:H.45, A:R.98 PO4.3: 5 residues within 4Å: Chain A: R.44, S.63, S.64, Q.65, R.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.63, A:S.64, A:S.64, A:R.98, A:R.98 Water bridges: A:R.44 PO4.4: 3 residues within 4Å: Chain A: D.144, A.145, Q.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.145, A:Q.146, A:Q.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oyen, D. et al., Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihyrofolate reductase of Escherichia coli. Biochim.Biophys.Acta (2013)

Release Date

2013-04-24

Peptides

Dihydrofolate reductase: A
Nb113 camelid antibody fragment: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Dihydrofolate reductase

Nb113 camelid antibody fragment

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