3VFK
The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier
- PDB DOI: https://doi.org/10.2210/pdb3VFK/pdb
- Classification: SUGAR BINDING PROTEIN/ANTIBIOTIC
- Organism(s): Homo sapiens, Actinoplanes teichomyceticus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-01-09 Released: 2013-01-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.306
- R-Value Work: 0.278
- R-Value Observed: 0.279
This is version 3.1 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 |
| ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala | 79 | Homo sapiens | Mutation(s): 0 Gene Names: UBC |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48 | |||||
PHAROS: P0CG48 GTEx: ENSG00000150991 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG48 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| MonodeChloro- Teicoplanin A2-2 | B [auth G] | 7 | Actinoplanes teichomyceticus | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| MAN Query on MAN | F [auth G] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | ||
| GCS Query on GCS | C [auth G] | 2-amino-2-deoxy-beta-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-QZABAPFNSA-N |  | ||
| T55 Query on T55 | D [auth G] | 8-METHYLNONANOIC ACID C10 H20 O2 OAOABCKPVCUNKO-UHFFFAOYSA-N |  | ||
| Modified Residues 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CCS Query on CCS | A | L-PEPTIDE LINKING | C5 H9 N O4 S |  | CYS |
| 3MY Query on 3MY | B [auth G] | D-PEPTIDE LINKING | C9 H10 Cl N O3 |  | TYR |
| OMX Query on OMX | B [auth G] | L-PEPTIDE LINKING | C9 H11 N O4 |  | TYR |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000882 Query on PRD_000882 | B [auth G] | MonodeChloro- Teicoplanin A2-2 | Glycopeptide / Antibiotic |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.306
- R-Value Work: 0.278
- R-Value Observed: 0.279
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.01 | α = 90 |
| b = 25.18 | β = 109.18 |
| c = 38.71 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MOLREP | phasing |
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2013-01-09 Deposition Author(s): Economou, N.J., Weeks, S.D., Grasty, K.C., Loll, P.J.
Revision History (Full details and data files)
- Version 1.0: 2013-01-09
Type: Initial release - Version 1.1: 2013-03-27
Changes: Structure summary - Version 1.2: 2013-04-03
Changes: Derived calculations - Version 1.3: 2013-06-19
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Polymer sequence, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary - Version 3.0: 2023-09-27
Changes: Polymer sequence - Version 3.1: 2023-12-06
Changes: Data collection, Derived calculations
