9D20 | pdb_00009d20

Crystal structure of DLK1 in complex with ACVR2B

PDB DOI: https://doi.org/10.2210/pdb9D20/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-08-08 Released: 2025-05-07
Deposition Author(s): Ming, Q., Antfolk, D., Luca, V.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.242 (Depositor), 0.238 (DCC)
R-Value Work:
0.212 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Molecular mechanism of Activin receptor inhibition by Delta-like non-canonical Notch ligand 1

Antfolk, D., Ming, Q., Luca, V.C.

To be published.

Macromolecule Content

Total Structure Weight: 41.98 kDa
Atom Count: 2,776
Modeled Residue Count: 346
Deposited Residue Count: 350
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-2B	A [auth E], C [auth A]	94	Homo sapiens	Mutation(s): 0 Gene Names: ACVR2B EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q13705 (Homo sapiens) Explore Q13705 Go to UniProtKB: Q13705
PHAROS: Q13705 GTEx: ENSG00000114739
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13705
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth E] Focus chain C [auth A]	Go to GlyGen: Q13705-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein delta homolog 1	B [auth D], D [auth B]	81	Homo sapiens	Mutation(s): 0 Gene Names: DLK1, DLK
UniProt & NIH Common Fund Data Resources
Find proteins for P80370 (Homo sapiens) Explore P80370 Go to UniProtKB: P80370
PHAROS: P80370 GTEx: ENSG00000185559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80370
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth D] Focus chain D [auth B]	Go to GlyGen: P80370-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E SDF format, chain F [auth E] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain E MOL2 format, chain F [auth E] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain E mmCIF format, chain F [auth E] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	E, F [auth E], O [auth A], P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E Focus chain F [auth E] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain E Focus chain F [auth E] Focus chain O [auth A] Focus chain P [auth A]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain T [auth B] MOL2 format, chain K [auth D] MOL2 format, chain T [auth B] mmCIF format, chain K [auth D] mmCIF format, chain T [auth B]	K [auth D], T [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain K [auth D] Focus chain T [auth B] Interactions & Density Focus chain K [auth D] Focus chain T [auth B]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain S [auth B] MOL2 format, chain J [auth D] MOL2 format, chain S [auth B] mmCIF format, chain J [auth D] mmCIF format, chain S [auth B]	J [auth D], S [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain J [auth D] Focus chain S [auth B] Interactions & Density Focus chain J [auth D] Focus chain S [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain I [auth E] SDF format, chain N [auth D] SDF format, chain R [auth A] SDF format, chain U [auth B] MOL2 format, chain H [auth E] MOL2 format, chain I [auth E] MOL2 format, chain N [auth D] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] mmCIF format, chain H [auth E] mmCIF format, chain I [auth E] mmCIF format, chain N [auth D] mmCIF format, chain R [auth A] mmCIF format, chain U [auth B]	H [auth E], I [auth E], N [auth D], R [auth A], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth E] Focus chain I [auth E] Focus chain N [auth D] Focus chain R [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth E] Focus chain I [auth E] Focus chain N [auth D] Focus chain R [auth A] Focus chain U [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain Q [auth A] MOL2 format, chain G [auth E] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth A] mmCIF format, chain G [auth E] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth A]	G [auth E], L [auth D], M [auth D], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain L [auth D] Focus chain M [auth D] Focus chain Q [auth A] Interactions & Density Focus chain G [auth E] Focus chain L [auth D] Focus chain M [auth D] Focus chain Q [auth A]