Download MendeleyThrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)
Sandner, A., Heine, A., Klebe, G.To be published.
6YHG
Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)
- PDB DOI: https://doi.org/10.2210/pdb6YHG/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No
- Deposited: 2020-03-29 Released: 2021-04-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.145
- R-Value Work: 0.123
- R-Value Observed: 0.124
Starting Model: experimental
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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 |
| Prothrombin | A [auth L] | 36 | 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 |
| Prothrombin | 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 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P00734-1 | ||||
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 7 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | G [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| DPN Query on DPN | I [auth H] | D-PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-MRVPVSSYSA-N |  | ||
| SZ4 Query on SZ4 | K [auth H] | 1-(3-methoxyphenyl)methanamine C8 H11 N O GRRIMVWABNHKBX-UHFFFAOYSA-N |  | ||
| PRO Query on PRO | J [auth H] | PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N |  | ||
| PO4 Query on PO4 | D [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | H | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth H], F [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 |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.145
- R-Value Work: 0.123
- R-Value Observed: 0.124
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.25 | α = 90 |
| b = 71.251 | β = 100.61 |
| c = 72.742 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| Coot | model building |
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2021-04-07 Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Collins, C.
Revision History (Full details and data files)
- Version 1.0: 2021-04-07
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-11-20
Changes: Structure summary
