3U98
Human Thrombin In Complex With MI001
- PDB DOI: https://doi.org/10.2210/pdb3U98/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No 
- Deposited: 2011-10-18 Released: 2012-10-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.187 
- R-Value Work: 0.164 
- R-Value Observed: 0.165 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Thrombin Light Chain | 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 |
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 |
Hirudin variant-2 | C [auth I] | 13 | 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 | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BJA Query on BJA | E [auth H] | (2S)-1-[(2R)-2-(benzylsulfonylamino)-5-guanidino-pentanoyl]-N-[(4-carbamimidoylphenyl)methyl]pyrrolidine-2-carboxamide C26 H36 N8 O4 S QKFCYPKTTJCUSZ-YADHBBJMSA-N | |||
NAG Query on NAG | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PO4 Query on PO4 | F [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
NA Query on NA | G [auth H], 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: 5 | |||||
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ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000877 (BJA) Query on PRD_000877 | E [auth H] | (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]PYRROLIDINE-2-CARBOXAMIDE | Peptide-like / Thrombin inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.187 
- R-Value Work: 0.164 
- R-Value Observed: 0.165 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 70.3 | α = 90 |
b = 71.5 | β = 100.4 |
c = 72.2 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
Revision History (Full details and data files)
- Version 1.0: 2012-10-24
Type: Initial release - Version 1.1: 2012-12-12
Changes: Other - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.4: 2023-12-06
Changes: Data collection