3VFJ
The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand carrier
- PDB DOI: https://doi.org/10.2210/pdb3VFJ/pdb
- Classification: SUGAR BINDING PROTEIN/ANTIBIOTIC
- Organism(s): Escherichia coli K-12, 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: 2.05 Å
- R-Value Free: 0.231 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
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 |
Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala | 378 | Escherichia coli K-12 | Mutation(s): 0  Gene Names: malE, b4034, JW3994 | ||
UniProt | |||||
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0AEX9 | ||||
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 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | P [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
MAN Query on MAN | Q [auth G] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N | |||
GCS Query on GCS | N [auth G] | 2-amino-2-deoxy-beta-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-QZABAPFNSA-N | |||
T55 Query on T55 | O [auth G] | 8-METHYLNONANOIC ACID C10 H20 O2 OAOABCKPVCUNKO-UHFFFAOYSA-N | |||
CAC Query on CAC | M [auth A], R [auth G] | CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M | |||
ZN Query on ZN | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
ACT Query on ACT | K [auth A], L [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
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: 2.05 Å
- R-Value Free: 0.231 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 40.32 | α = 90 |
b = 123.61 | β = 90 |
c = 156.74 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
MOLREP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
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: 2013-03-06
Changes: Structure summary - Version 1.2: 2013-03-13
Changes: Structure summary - Version 1.3: 2013-03-27
Changes: Derived calculations - Version 1.4: 2013-04-03
Changes: Derived calculations - Version 1.5: 2013-06-19
Changes: Database references - Version 1.6: 2014-12-10
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Polymer sequence, Structure summary