Macromolecule Content

Total Structure Weight: 424.23 kDa
Atom Count: 31709
Modelled Residue Count: 3696
Deposited Residue Count: 3732
Unique protein chains: 1

2DCN

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)

DOI: 10.2210/pdb2DCN/pdb

Classification: TRANSFERASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-01-10 Released: 2006-01-31
Deposition Author(s): Okazaki, S., Onda, H., Suzuki, A., Kuramitsu, S., Masui, R., Yamane, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate

Okazaki, S., Onda, H., Suzuki, A., Kuramitsu, S., Masui, R., Yamane, T.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical fructokinase	A, B, C, D, E, F, G, H,	A, B, C, D, E, F, G, H, I, J, K, L	311	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: kdgK, ST2478, STK_24780 EC: 2.7.1.45
Find proteins for Q96XN9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96XN9 Go to UniProtKB: Q96XN9
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [B] SDF format, chain AC [J] SDF format, chain GA [C] SDF format, chain GC [K] SDF format, chain HB [G] SDF format, chain NA [D] SDF format, chain NB [H] SDF format, chain NC [L] SDF format, chain T [A] SDF format, chain TA [E] SDF format, chain TB [I] SDF format, chain YA [F] MOL2 format, chain AA [B] MOL2 format, chain AC [J] MOL2 format, chain GA [C] MOL2 format, chain GC [K] MOL2 format, chain HB [G] MOL2 format, chain NA [D] MOL2 format, chain NB [H] MOL2 format, chain NC [L] MOL2 format, chain T [A] MOL2 format, chain TA [E] MOL2 format, chain TB [I] MOL2 format, chain YA [F]	A, B, C, D, E, F, G, H, I, J, K, L	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
CKP Query on CKP Download Ideal Coordinates CCD File SDF format, chain FA [C] SDF format, chain FC [K] SDF format, chain GB [G] SDF format, chain MA [D] SDF format, chain MB [H] SDF format, chain MC [L] SDF format, chain S [A] SDF format, chain SA [E] SDF format, chain SB [I] SDF format, chain XA [F] SDF format, chain Z [B] SDF format, chain ZB [J] MOL2 format, chain FA [C] MOL2 format, chain FC [K] MOL2 format, chain GB [G] MOL2 format, chain MA [D] MOL2 format, chain MB [H] MOL2 format, chain MC [L] MOL2 format, chain S [A] MOL2 format, chain SA [E] MOL2 format, chain SB [I] MOL2 format, chain XA [F] MOL2 format, chain Z [B] MOL2 format, chain ZB [J]	A, B, C, D, E, F, G, H, I, J, K, L	6-O-phosphono-beta-D-psicofuranosonic acid C₆ H₁₁ O₁₀ P LXQWHMQOSMCJIZ-ZGEUXELVSA-N		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [C] SDF format, chain EC [K] SDF format, chain FB [G] SDF format, chain LA [D] SDF format, chain LB [H] SDF format, chain LC [L] SDF format, chain R [A] SDF format, chain RA [E] SDF format, chain RB [I] SDF format, chain WA [F] SDF format, chain Y [B] SDF format, chain YB [J] MOL2 format, chain EA [C] MOL2 format, chain EC [K] MOL2 format, chain FB [G] MOL2 format, chain LA [D] MOL2 format, chain LB [H] MOL2 format, chain LC [L] MOL2 format, chain R [A] MOL2 format, chain RA [E] MOL2 format, chain RB [I] MOL2 format, chain WA [F] MOL2 format, chain Y [B] MOL2 format, chain YB [J]	A, B, C, D, E, F, G, H, I, J, K, L	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [G] SDF format, chain BA [C] SDF format, chain BB [G] SDF format, chain BC [K] SDF format, chain CA [C] SDF format, chain CB [G] SDF format, chain CC [K] SDF format, chain DA [C] SDF format, chain DB [G] SDF format, chain DC [K] SDF format, chain EB [G] SDF format, chain HA [D] SDF format, chain HC [L] SDF format, chain IA [D] SDF format, chain IB [H] SDF format, chain IC [L] SDF format, chain JA [D] SDF format, chain JB [H] SDF format, chain JC [L] SDF format, chain KA [D] SDF format, chain KB [H] SDF format, chain KC [L] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain OA [E] SDF format, chain OB [I] SDF format, chain P [A] SDF format, chain PA [E] SDF format, chain PB [I] SDF format, chain Q [A] SDF format, chain QA [E] SDF format, chain QB [I] SDF format, chain U [B] SDF format, chain UA [F] SDF format, chain UB [J] SDF format, chain V [B] SDF format, chain VA [F] SDF format, chain VB [J] SDF format, chain W [B] SDF format, chain WB [J] SDF format, chain X [B] SDF format, chain XB [J] SDF format, chain ZA [G] MOL2 format, chain AB [G] MOL2 format, chain BA [C] MOL2 format, chain BB [G] MOL2 format, chain BC [K] MOL2 format, chain CA [C] MOL2 format, chain CB [G] MOL2 format, chain CC [K] MOL2 format, chain DA [C] MOL2 format, chain DB [G] MOL2 format, chain DC [K] MOL2 format, chain EB [G] MOL2 format, chain HA [D] MOL2 format, chain HC [L] MOL2 format, chain IA [D] MOL2 format, chain IB [H] MOL2 format, chain IC [L] MOL2 format, chain JA [D] MOL2 format, chain JB [H] MOL2 format, chain JC [L] MOL2 format, chain KA [D] MOL2 format, chain KB [H] MOL2 format, chain KC [L] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain OA [E] MOL2 format, chain OB [I] MOL2 format, chain P [A] MOL2 format, chain PA [E] MOL2 format, chain PB [I] MOL2 format, chain Q [A] MOL2 format, chain QA [E] MOL2 format, chain QB [I] MOL2 format, chain U [B] MOL2 format, chain UA [F] MOL2 format, chain UB [J] MOL2 format, chain V [B] MOL2 format, chain VA [F] MOL2 format, chain VB [J] MOL2 format, chain W [B] MOL2 format, chain WB [J] MOL2 format, chain X [B] MOL2 format, chain XB [J] MOL2 format, chain ZA [G]	A, B, C, D, E, F, G, H, I, J, K, L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.178
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.638	α = 90
b = 150.229	β = 93.73
c = 154.757	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

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Entry History

Deposition Data

Deposited Date: 2006-01-10
Released Date: 2006-01-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-05-24
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Derived calculations, Structure summary

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