3U8T
Human thrombin complexed with D-Phe-Pro-D-Arg-Cys
- PDB DOI: https://doi.org/10.2210/pdb3U8T/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2011-10-17 Released: 2012-04-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.195
- R-Value Work: 0.153
- R-Value Observed: 0.155
This is version 1.3 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thrombin light chain | A [auth L] | 27 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.5 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734 | |||||
PHAROS: P00734 GTEx: ENSG00000180210 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
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 |
| Thrombin heavy chain | B [auth H] | 259 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.5 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734 | |||||
PHAROS: P00734 GTEx: ENSG00000180210 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| D-PHE-PRO-D-ARG-CYS DIRECT THROMBIN INHIBITOR | C [auth I] | 5 | N/A | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| IOD Query on IOD | F [auth H] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M |  | ||
| MPD Query on MPD | H | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| CL Query on CL | G [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | E [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_001092 Query on PRD_001092 | C [auth I] | D-phenylalanyl-L-prolyl-N~5~-[amino(iminio)methyl]-D-ornithyl-L-cysteinamide | Peptide-like / Thrombin inhibitor |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.195
- R-Value Work: 0.153
- R-Value Observed: 0.155
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.15785/SBGRID/106
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.8 | α = 90 |
| b = 77.1 | β = 90 |
| c = 83.43 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2012-04-11 Deposition Author(s): Figueiredo, A.C., Clement, C.C., Philipp, M., Pereira, P.J.B.
Revision History (Full details and data files)
- Version 1.0: 2012-04-11
Type: Initial release - Version 1.1: 2012-12-12
Changes: Other - Version 1.2: 2013-06-05
Changes: Other - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
