Download MendeleyStructure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria.
Thanuja, G., Ramaswamy, S.(2020) ACS Omega 5: 30923-30926
6JDB
Crystal structure of N-acetyl mannosmaine kinase in complex with ManNAc-6P and ADP from Haemophilus influenzae
- PDB DOI: https://doi.org/10.2210/pdb6JDB/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Haemophilus influenzae 86-028NP
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-02-01 Released: 2020-02-05
- Funding Organization(s): Department of Biotechnology (India)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.276
- R-Value Work: 0.213
- R-Value Observed: 0.216
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| N-acetylmannosamine kinase | 290 | Haemophilus influenzae 86-028NP | Mutation(s): 0 Gene Names: nanK EC: 2.7.1.60 |  | |
UniProt | |||||
Find proteins for Q4QP43 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QP43 Go to UniProtKB: Q4QP43 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q4QP43 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADP (Subject of Investigation/LOI) Query on ADP | B [auth A] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| BMX (Subject of Investigation/LOI) Query on BMX | C [auth A] | 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose C8 H16 N O9 P BRGMHAYQAZFZDJ-UOLFYFMNSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.276
- R-Value Work: 0.213
- R-Value Observed: 0.216
- Space Group: I 41 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 92.591 | α = 90 |
| b = 92.591 | β = 90 |
| c = 183.321 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Aimless | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-02-05 Deposition Author(s): Thanuja, G., Ramaswamy, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Biotechnology (India) | India | BT/IN/Sweden/06/SR/2017-18 |
| Department of Biotechnology (India) | India | BT/PR12422/MED/31/287/ 2014 |
Revision History (Full details and data files)
- Version 1.0: 2020-02-05
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2020-12-16
Changes: Database references, Structure summary - Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description
