Download MendeleyThrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
Marca, A., Sandner, A., Heine, A., Klebe, G.To be published.
5MM6
Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
- PDB DOI: https://doi.org/10.2210/pdb5MM6/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens, Hirudo medicinalis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2016-12-08 Released: 2017-12-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 ?
- R-Value Free: 0.142
- R-Value Work: 0.123
- R-Value Observed: 0.124
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 |
| Thrombin light chain | A [auth L] | 36 | Homo sapiens | Mutation(s): 0 Gene Names: F2 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:
(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): 1 Gene Names: F2 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 |
| Hirudin variant-2 | C [auth I] | 12 | Hirudo medicinalis | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P09945 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 32U Query on 32U | N [auth H] | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide C22 H28 N5 O2 VZFTWWJAUZOJDH-MOPGFXCFSA-O |  | ||
| PO4 Query on PO4 | I [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | D [auth H], E [auth H], F [auth H], J [auth H], M [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | G [auth H], H | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| NA Query on NA | K [auth H], L [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TYS Query on TYS | C [auth I] | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000600 (32U) Query on PRD_000600 | N [auth H] | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide | Peptide-like / Thrombin inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.29 ?
- R-Value Free: 0.142
- R-Value Work: 0.123
- R-Value Observed: 0.124
- Space Group: C 1 2 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 70.344 | ¦Á = 90 |
| b = 71.649 | ¦Â = 100.48 |
| c = 72.538 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-12-20 Deposition Author(s): Marca, A., Sandner, A., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2017-12-20
Type: Initial release - Version 1.1: 2018-06-27
Changes: Data collection, Structure summary - Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
