4LZ4
X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase
- PDB DOI: https://doi.org/10.2210/pdb4LZ4/pdb
- NAKB: 4LZ4
- Classification: HYDROLASE/HYDROLASE INHIBITOR/DNA
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2013-07-31 Released: 2014-01-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.56 Å
- R-Value Free: 0.227 
- R-Value Work: 0.168 
- R-Value Observed: 0.171 
This is version 2.0 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 | 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 | 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 | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
0G6 Query on 0G6 | H [auth B], K [auth D] | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O | |||
NAG Query on NAG | G [auth B], J [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
K Query on K | M [auth E], N [auth F] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
NA Query on NA | I [auth B], L [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000020 (0G6) Query on PRD_000020 | H [auth B], K [auth D] | D-Phe-Pro-Arg-CH2Cl | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.56 Å
- R-Value Free: 0.227 
- R-Value Work: 0.168 
- R-Value Observed: 0.171 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.736 | α = 90 |
b = 120.725 | β = 94.22 |
c = 67.233 | γ = 90 |
Software Name | Purpose |
---|---|
CCP4 | refinement |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-01-08  Deposition Author(s): Pica, A., Russo Krauss, I., Merlino, A., Sica, F.
Revision History (Full details and data files)
- Version 1.0: 2014-01-08
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary