Download MendeleyCrystal structure of proteinase K inhibited by a lactoferrin octapeptide Gly-Asp-Glu-Gln-Gly-Glu-Asn-Lys at 2.15 A resolution
Prem Kumar, R., Singh, A.K., Singh, N., Kaur, P., Sharma, S., Singh, T.P.To be published.
2HD4 | pdb_00002hd4
Crystal structure of proteinase K inhibited by a lactoferrin octapeptide Gly-Asp-Glu-Gln-Gly-Glu-Asn-Lys at 2.15 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2HD4/pdb
- Classification: HYDROLASE
- Organism(s): Parengyodontium album, Homo sapiens
- Mutation(s): No
- Deposited: 2006-06-20 Released: 2006-07-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.202 (Depositor)
- R-Value Work: 0.171 (Depositor)
- R-Value Observed: 0.172 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 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 |
| Proteinase K | 279 | Parengyodontium album | Mutation(s): 0 EC: 3.4.21.64 |  | |
UniProt | |||||
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06873 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 8-mer Peptide from Lactotransferrin | 8 | N/A | Mutation(s): 0 EC: 3.4.21 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02788 (Homo sapiens) Explore P02788 Go to UniProtKB: P02788 | |||||
PHAROS: P02788 GTEx: ENSG00000012223 | |||||
Entity Groups | |||||
| UniProt Group | P02788 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACY Query on ACY | D [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.202 (Depositor)
- R-Value Work: 0.171 (Depositor)
- R-Value Observed: 0.172 (Depositor)
Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.366 | α = 90 |
| b = 68.366 | β = 90 |
| c = 108.079 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2006-07-04 Deposition Author(s): Prem Kumar, R., Singh, A.K., Singh, N., Kaur, P., Sharma, S., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2006-07-04
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2024-10-30
Changes: Structure summary
