Download MendeleyStructural basis for the substrate specificity of bone morphogenetic protein 1/tolloid-like metalloproteases
Mac Sweeney, A., Parrado, S.G., Vinzenz, D., Bernardi, A., Hein, A., Bodendorf, U., Erbel, P., Logel, C., Gerhartz, B.To be published.
3EDH | pdb_00003edh
Crystal structure of bone morphogenetic protein 1 protease domain in complex with partially bound DMSO
- PDB DOI: https://doi.org/10.2210/pdb3EDH/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-09-03 Released: 2008-09-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.172 (Depositor), 0.170 (DCC)
- R-Value Work: 0.140 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.142 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Bone morphogenetic protein 1 | 201 | Homo sapiens | Mutation(s): 0 Gene Names: BMP1, PCOLC EC: 3.4.24.19 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P13497 (Homo sapiens) Explore P13497 Go to UniProtKB: P13497 | |||||
PHAROS: P13497 GTEx: ENSG00000168487 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13497 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DMS Query on DMS | E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| ACE Query on ACE | B [auth A] | ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.172 (Depositor), 0.170 (DCC)
- R-Value Work: 0.140 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.142 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.499 | α = 90 |
| b = 59.093 | β = 90 |
| c = 69.451 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2008-09-16 Deposition Author(s): Mac Sweeney, A.
Revision History (Full details and data files)
- Version 1.0: 2008-09-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
