3DUV
Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the-configuration
- PDB DOI: https://doi.org/10.2210/pdb3DUV/pdb
- Classification: TRANSFERASE
- Organism(s): Haemophilus influenzae
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2008-07-18 Released: 2008-12-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236 
- R-Value Work: 0.170 
- R-Value Observed: 0.177 
This is version 1.2 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 |
3-deoxy-manno-octulosonate cytidylyltransferase | 262 | Haemophilus influenzae | Mutation(s): 0  Gene Names: kdsB EC: 2.7.7.38 | ||
UniProt | |||||
Find proteins for P44490 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44490  Go to UniProtKB:  P44490 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P44490 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
P4C Query on P4C | D [auth A] | O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C14 H28 O8 CTLLATPOKUEFSQ-UHFFFAOYSA-N | |||
KDO Query on KDO | C [auth A], E [auth B] | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C8 H14 O8 NNLZBVFSCVTSLA-HXUQBWEZSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.236 
- R-Value Work: 0.170 
- R-Value Observed: 0.177 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 48.418 | α = 90 |
b = 82.609 | β = 90 |
c = 115.712 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2008-12-09  Deposition Author(s): Yoon, H.J., Ku, M.J., Mikami, B., Suh, S.W.
Revision History (Full details and data files)
- Version 1.0: 2008-12-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary