6GBW
Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-arginyl)pyrrolidine-2-carboxamide)
- PDB DOI: https://doi.org/10.2210/pdb6GBW/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens, Hirudo medicinalis
- Mutation(s): No 
- Deposited: 2018-04-16 Released: 2019-04-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.165 
- R-Value Work: 0.132 
- R-Value Observed: 0.134 
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 |
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 | |||||
|
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 | ||||
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 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EU5 Query on EU5 | I [auth H] | (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{S})-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]pyrrolidine-2-carboxamide C26 H36 Cl N7 O4 S MWLLGEVAEDIFRC-GOTSBHOMSA-N | |||
NAG Query on NAG | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
DMS Query on DMS | G [auth H], H | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-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: 1.45 Å
- R-Value Free: 0.165 
- R-Value Work: 0.132 
- R-Value Observed: 0.134 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.84 | α = 90 |
b = 71.119 | β = 100.58 |
c = 72.858 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
Coot | model building |
XDS | data scaling |
PHASER | phasing |
XDS | data reduction |
Entry History 
Deposition Data
- Released Date: 2019-04-24  Deposition Author(s): Sandner, A., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2019-04-24
Type: Initial release - Version 1.1: 2019-11-27
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary