SMTL ID : 8q6k.1

Human IgD Fab in complex with an orthosteric inhibitor of Phl p 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.154, D.156, S.197, E.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.156, A:S.197 EDO.2: 4 residues within 4Å: Chain B: E.46, W.47, S.61, K.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.46, B:W.47, B:S.61 Water bridges: B:W.47, B:W.47 EDO.3: 7 residues within 4Å: Chain B: R.38, Q.39, A.40, H.43, R.44, E.46 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:A.40, B:R.44, B:E.46 EDO.4: 4 residues within 4Å: Chain B: P.144, P.194, L.195, Q.196 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: E.128 Chain B: D.128, V.129, F.130, K.216 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.128, B:V.129, B:V.129, B:K.216 EDO.6: 6 residues within 4Å: Chain B: R.38, E.46, K.63, R.67, D.90 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:E.46, B:R.67, B:D.90 EDO.7: 6 residues within 4Å: Chain A: Q.172, S.173, N.174 Chain B: Q.172, R.173, T.174 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.173, B:T.174 Water bridges: A:D.143, A:D.143, A:N.174, A:N.174, B:Q.172 EDO.8: 4 residues within 4Å: Chain B: Q.39, A.40, P.41, V.93 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain B: S.120, H.155, Q.179, Y.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.120, B:Y.185, B:Y.185 EDO.13: 4 residues within 4Å: Chain B: N.57 Chain C: F.30, D.31, D.32 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.57, C:D.31, C:D.32

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 6 residues within 4Å: Chain A: E.165, S.184 Chain B: R.180, R.181, D.182, M.186 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.180, B:R.181 Hydrogen bonds: B:R.181, A:E.165, A:S.184 Salt bridges: B:R.180 ACT.11: 2 residues within 4Å: Chain B: Y.102, S.103 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.103 Water bridges: B:Y.102, A:D.34

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 1 residues within 4Å: Chain B: Y.164 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vester, S.K. et al., Expanding the Anti-Phl p 7 Antibody Toolkit: An Anti-Idiotype Nanobody Inhibitor. Antibodies (2023)

Release Date

2023-12-06

Peptides

Human IgD Fab light chain: A
Human IgD Fab heavy chain: B
Nanobody 072: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
N

Human IgD Fab light chain

Human IgD Fab heavy chain

Nanobody 072

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