6P2R
Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt2 complex bound to the sugar donor
- PDB DOI: https://doi.org/10.2210/pdb6P2R/pdb
- EM Map EMD-20240: EMDB EMDataResource
- Classification: TRANSFERASE
- Organism(s): Saccharomyces cerevisiae W303
- Expression System: Saccharomyces cerevisiae W303
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2019-05-21 Released: 2019-07-10 
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
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 |
Dolichyl-phosphate-mannose--protein mannosyltransferase 1 | 817 | Saccharomyces cerevisiae W303 | Mutation(s): 0  Gene Names: PMT1, YDL095W, D2390 EC: 2.4.1.109 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P33775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33775  Go to UniProtKB:  P33775 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P33775 | ||||
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 |
Dolichyl-phosphate-mannose--protein mannosyltransferase 2 | 759 | Saccharomyces cerevisiae W303 | Mutation(s): 0  Gene Names: PMT2, FUN25, YAL023C EC: 2.4.1.109 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P31382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31382  Go to UniProtKB:  P31382 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P31382 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CPL Query on CPL | D [auth A], G [auth B], H [auth B] | 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C42 H80 N O8 P JLPULHDHAOZNQI-ZTIMHPMXSA-N | |||
NNM (Subject of Investigation/LOI) Query on NNM | E [auth A] | (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate C40 H69 O4 P CTKMEBTWSXRRSJ-RRHRGVEJSA-N | |||
NAG Query on NAG | C [auth A], F [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | |
MODEL REFINEMENT | Coot | |
RECONSTRUCTION | Coot | |
RECONSTRUCTION | UCSF Chimera |
Entry History & Funding Information
Deposition Data
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | R01-CA231466 |
Revision History (Full details and data files)
- Version 1.0: 2019-07-10
Type: Initial release - Version 1.1: 2019-07-24
Changes: Data collection, Database references - Version 1.2: 2019-08-21
Changes: Data collection, Database references - Version 1.3: 2019-12-04
Changes: Author supporting evidence - Version 1.4: 2019-12-18
Changes: Other - Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary