5LU8
CRYSTAL STRUCTURE OF YVAD-CMK BOUND HUMAN LEGUMAIN (AEP) IN COMPLEX WITH COMPOUND 11B
- PDB DOI: https://doi.org/10.2210/pdb5LU8/pdb
- Classification: HYDROLASE
- Organism(s): synthetic construct, Homo sapiens
- Expression System: Leishmania tarentolae
- Mutation(s): Yes
- Deposited: 2016-09-08 Released: 2017-03-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.251
- R-Value Work: 0.219
- R-Value Observed: 0.220
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE | A [auth C] | 6 | synthetic construct | Mutation(s): 0 |  |
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 |
| Legumain | B [auth A] | 263 | Homo sapiens | Mutation(s): 1 Gene Names: LGMN, PRSC1 EC: 3.4.22.34 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q99538 (Homo sapiens) Explore Q99538 Go to UniProtKB: Q99538 | |||||
PHAROS: Q99538 GTEx: ENSG00000100600 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99538 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 5KN Query on 5KN | H [auth A] | 2,4-di(morpholin-4-yl)aniline C14 H21 N3 O2 VEMKXLKXBFHADY-UHFFFAOYSA-N |  | ||
| EMC Query on EMC | G [auth A] | ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | E [auth A], F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SNN Query on SNN | B [auth A] | L-PEPTIDE LINKING | C4 H6 N2 O2 |  | ASN |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_002086 Query on PRD_002086 | A [auth C] | ACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE | Peptide-like / Inhibitor |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.251
- R-Value Work: 0.219
- R-Value Observed: 0.220
- Space Group: P 42
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.32 | α = 90 |
| b = 64.32 | β = 90 |
| c = 78.91 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-03-29 Deposition Author(s): Dall, E., Ye, K., Brandstetter, H.
Revision History (Full details and data files)
- Version 1.0: 2017-03-29
Type: Initial release - Version 1.1: 2017-04-05
Changes: Database references - Version 1.2: 2018-06-13
Changes: Data collection, Structure summary - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Refinement description
