SMTL ID : 9d20.1 (1 other biounit)

Crystal structure of DLK1 in complex with ACVR2B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: W.39, N.41, Y.76, H.91 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.39, A:Y.76, A:H.91 NAG.2: 2 residues within 4Å: Chain A: R.16, N.18 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain A: R.88, F.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.89 EDO.8: 2 residues within 4Å: Chain B: D.32, S.36 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.36 EDO.9: 4 residues within 4Å: Chain B: R.37, P.38, V.39, T.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.37, B:P.38, B:T.40, B:T.40

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

SO4.4: 3 residues within 4Å: Chain A: N.41, S.42, S.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.43 SO4.5: 8 residues within 4Å: Chain A: N.59, R.63, V.67, T.69, F.77, C.78, C.79 Chain B: R.23 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.59, A:V.67, A:T.69, A:C.79 Salt bridges: A:R.63, B:R.23 SO4.10: 3 residues within 4Å: Chain A: R.32 Chain B: T.57, Q.58 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.58, A:R.32

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.6: 1 residues within 4Å: Chain B: T.52 No protein-ligand interaction detected (PLIP)

1 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.7: 5 residues within 4Å: Chain B: P.38, V.39, T.40, N.41, S.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antfolk, D. et al., Molecular mechanism of Activin receptor inhibition by Delta-like non-canonical Notch ligand 1. To Be Published

Release Date

2025-05-07

Peptides

Activin receptor type-2B: A
Protein delta homolog 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
D

Activin receptor type-2B

Protein delta homolog 1

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