2D1K
Ternary complex of the WH2 domain of mim with actin-dnase I
- PDB DOI: https://doi.org/10.2210/pdb2D1K/pdb
- Classification: STRUCTURAL PROTEIN
- Organism(s): Oryctolagus cuniculus, Bos taurus, Homo sapiens
- Mutation(s): Yes 
- Deposited: 2005-08-26 Released: 2006-09-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.284 
- R-Value Work: 0.217 
- R-Value Observed: 0.220 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Actin, alpha skeletal muscle | 375 | Oryctolagus cuniculus | Mutation(s): 1  | ||
UniProt | |||||
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P68135 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Deoxyribonuclease-1 | 260 | Bos taurus | Mutation(s): 0  EC: 3.1.21.1 | ||
UniProt | |||||
Find proteins for P00639 (Bos taurus) Explore P00639  Go to UniProtKB:  P00639 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00639 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Metastasis suppressor protein 1 | 32 | N/A | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O43312 (Homo sapiens) Explore O43312  Go to UniProtKB:  O43312 | |||||
PHAROS:  O43312 GTEx:  ENSG00000170873  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O43312 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ATP Query on ATP | F [auth A] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N | |||
CA Query on CA | E [auth A], G [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
MG Query on MG | H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
HIC Query on HIC | A | L-PEPTIDE LINKING | C7 H11 N3 O2 | HIS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.284 
- R-Value Work: 0.217 
- R-Value Observed: 0.220 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42.093 | α = 90 |
b = 75.487 | β = 90 |
c = 228.991 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2006-09-12  Deposition Author(s): Chereau, D., Kerff, F., Dominguez, R.
Revision History (Full details and data files)
- Version 1.0: 2006-09-12
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary