3RMM
Human Thrombin in complex with MI332
- PDB DOI: https://doi.org/10.2210/pdb3RMM/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No 
- Deposited: 2011-04-21 Released: 2012-04-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.179 
- R-Value Work: 0.155 
- R-Value Observed: 0.156 
This is version 1.5 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 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
M32 Query on M32 | E [auth H] | N-(benzylsulfonyl)-D-alanyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide C23 H29 Cl N4 O4 S MAUGNQAVJWFOOZ-IERDGZPVSA-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 | H | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GOL Query on GOL | F [auth H], G [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
NA Query on NA | I [auth H], J [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: 5 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000964 (M32) Query on PRD_000964 | E [auth H] | N-(BENZYLSULFONYL)-D-ALANYL-N-[2-(AMINOMETHYL)-5-CHLOROBENZYL]-L-PROLINAMIDE | Peptide-like / Thrombin inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.179 
- R-Value Work: 0.155 
- R-Value Observed: 0.156 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 70.1 | α = 90 |
b = 71.1 | β = 100.4 |
c = 72.7 | 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: 2012-04-25
Type: Initial release - Version 1.1: 2012-12-12
Changes: Other - Version 1.2: 2016-07-13
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary - Version 1.5: 2023-12-06
Changes: Data collection