4GWM
Crystal structure of human promeprin beta
- PDB DOI: https://doi.org/10.2210/pdb4GWM/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Membrane Protein: Yes  mpstruc
- Deposited: 2012-09-03 Released: 2012-09-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.188 
- R-Value Work: 0.168 
- R-Value Observed: 0.168 
This is version 2.0 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 |
Meprin A subunit beta | 592 | Homo sapiens | Mutation(s): 2  Gene Names: MEP1B EC: 3.4.24.63 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q16820 (Homo sapiens) Explore Q16820  Go to UniProtKB:  Q16820 | |||||
PHAROS:  Q16820 GTEx:  ENSG00000141434  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q16820 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, G | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | D | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G11460AB GlyCosmos:  G11460AB GlyGen:  G11460AB |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, L | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F, K | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G37135JQ GlyCosmos:  G37135JQ GlyGen:  G37135JQ |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | I | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G17601US GlyCosmos:  G17601US GlyGen:  G17601US |
Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | J | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G63564LA GlyCosmos:  G63564LA |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | O [auth A], U [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | R [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | M [auth A], S [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CL Query on CL | P [auth A], Q [auth A], V [auth B], W [auth B], X [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | N [auth A], T [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.188 
- R-Value Work: 0.168 
- R-Value Observed: 0.168 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.62 | α = 74.87 |
b = 71.12 | β = 80.08 |
c = 85.74 | γ = 65.13 |
Software Name | Purpose |
---|---|
ProDC | data collection |
SHELXS | phasing |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-09-19  Deposition Author(s): Arolas, J.L., Broder, C., Jefferson, T., Guevara, T., Sterchi, E.E., Bode, W., Stocker, W., Becker-Pauly, C., Gomis-Ruth, F.X.
Revision History (Full details and data files)
- Version 1.0: 2012-09-19
Type: Initial release - Version 1.1: 2012-10-31
Changes: Database references - Version 1.2: 2017-11-15
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary