SMTL ID : 7v5n.2 (1 other biounit)

Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Q.37, K.45, L.47, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.37, A:K.45, A:R.61, A:E.81 EDO.2: 3 residues within 4Å: Chain A: P.8, S.9, S.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.9, A:S.9 EDO.3: 3 residues within 4Å: Chain A: Y.32, S.92, T.93 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: S.60, R.61, S.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.60, A:S.76, A:S.76 Water bridges: A:R.61 EDO.5: 6 residues within 4Å: Chain A: Q.38, K.39, P.40, A.84, T.85, K.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.38, A:T.85, A:T.85 Water bridges: A:G.41, A:A.84, A:V.104 EDO.6: 4 residues within 4Å: Chain A: V.163, T.164, E.165 Chain B: P.177 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: T.178 Chain B: L.151, V.179, S.187, L.188, S.189 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.178, B:S.189 Water bridges: A:S.176, B:S.189, B:S.189 EDO.10: 6 residues within 4Å: Chain B: E.158, P.159, V.160, P.177, A.178, L.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.160, B:V.160, B:A.178 EDO.11: 4 residues within 4Å: Chain B: T.53, Y.54, T.55, T.74 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.55 Water bridges: B:T.74, B:T.74 EDO.13: 2 residues within 4Å: Chain C: T.21, C.22 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: N.137, N.138 Chain B: G.172, H.174 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.137, A:N.138, A:N.138 Water bridges: A:D.167, A:D.167, B:V.173 Salt bridges: B:H.174 SO4.12: 3 residues within 4Å: Chain B: R.66, R.67, R.87 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.67, B:R.67 Salt bridges: B:R.66, B:R.67, B:R.87

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 5 residues within 4Å: Chain A: Y.32, Y.91, S.92 Chain B: S.106, W.108 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.92 pi-Stacking: B:W.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saito, T. et al., Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection. Biosens.Bioelectron. (2022)

Release Date

2022-02-02

Peptides

bevacizumab fab light chain: A
bevacizumab fab heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

bevacizumab fab light chain

bevacizumab fab heavy chain

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