SMTL ID : 7lfd.1

Fab 7D6 bound to ApoL1 BH3 like peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 6 residues within 4Å: Chain A: G.13, V.14, Q.15, K.16 Chain B: N.52, T.55 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.13, A:K.16, B:N.52, B:N.54 Water bridges: A:Q.15, A:K.16 Salt bridges: A:K.16

1 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 7 residues within 4Å: Chain B: S.7, G.8, D.10, V.18, K.19, I.20, T.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.8

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain B: I.100, D.102, Y.105, I.106, S.107 Chain C: L.46, Y.49 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.100 GOL.4: 4 residues within 4Å: Chain B: L.72, E.73, T.74, S.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.74, B:S.75, B:S.75 GOL.5: 4 residues within 4Å: Chain B: K.137 Chain C: T.206, K.207, S.208 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.208, C:S.208 Water bridges: C:K.207

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.6: 4 residues within 4Å: Chain B: Q.39 Chain C: R.38, T.85, Y.87 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.38, C:Y.87, C:Y.87 Water bridges: C:T.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ultsch, M. et al., Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Commun Biol (2021)

Release Date

2021-08-04

Peptides

Apolipoprotein L1 BH3 like peptide: A
Fab 7D6 heavy chain: B
Fab 7D6 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Apolipoprotein L1 BH3 like peptide

Fab 7D6 heavy chain

Fab 7D6 light chain

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