2DCN | pdb_00002dcn

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

PDB DOI: https://doi.org/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 (Depositor), 0.228 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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.

Macromolecule Content

Total Structure Weight: 424.23 kDa
Atom Count: 31,709
Modeled Residue Count: 3,696
Deposited Residue Count: 3,732
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical fructokinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	311	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 EC: 2.7.1.45
UniProt
Find proteins for Q96XN9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96XN9 Go to UniProtKB: Q96XN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96XN9
Sequence Annotations 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 [auth B] SDF format, chain AC [auth J] SDF format, chain GA [auth C] SDF format, chain GC [auth K] SDF format, chain HB [auth G] SDF format, chain NA [auth D] SDF format, chain NB [auth H] SDF format, chain NC [auth L] SDF format, chain T [auth A] SDF format, chain TA [auth E] SDF format, chain TB [auth I] SDF format, chain YA [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GC [auth K] MOL2 format, chain HB [auth G] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth H] MOL2 format, chain NC [auth L] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth I] MOL2 format, chain YA [auth F] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GC [auth K] mmCIF format, chain HB [auth G] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth H] mmCIF format, chain NC [auth L] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth I] mmCIF format, chain YA [auth F]	AA [auth B] AC [auth J] GA [auth C] GC [auth K] HB [auth G] AA [auth B], AC [auth J], GA [auth C], GC [auth K], HB [auth G], NA [auth D], NB [auth H], NC [auth L], T [auth A], TA [auth E], TB [auth I], YA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth B] Focus chain AC [auth J] Focus chain GA [auth C] Focus chain GC [auth K] Focus chain HB [auth G] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain NC [auth L] Focus chain T [auth A] Focus chain TA [auth E] Focus chain TB [auth I] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth J] Focus chain GA [auth C] Focus chain GC [auth K] Focus chain HB [auth G] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain NC [auth L] Focus chain T [auth A] Focus chain TA [auth E] Focus chain TB [auth I] Focus chain YA [auth F]
CKP Query on CKP Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain FC [auth K] SDF format, chain GB [auth G] SDF format, chain MA [auth D] SDF format, chain MB [auth H] SDF format, chain MC [auth L] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain SB [auth I] SDF format, chain XA [auth F] SDF format, chain Z [auth B] SDF format, chain ZB [auth J] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth K] MOL2 format, chain GB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth H] MOL2 format, chain MC [auth L] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth I] MOL2 format, chain XA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth J] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth K] mmCIF format, chain GB [auth G] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth H] mmCIF format, chain MC [auth L] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth I] mmCIF format, chain XA [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain ZB [auth J]	FA [auth C] FC [auth K] GB [auth G] MA [auth D] MB [auth H] FA [auth C], FC [auth K], GB [auth G], MA [auth D], MB [auth H], MC [auth L], S [auth A], SA [auth E], SB [auth I], XA [auth F], Z [auth B], ZB [auth J]	6-O-phosphono-beta-D-psicofuranosonic acid C₆ H₁₁ O₁₀ P LXQWHMQOSMCJIZ-ZGEUXELVSA-N		Interactions Focus chain FA [auth C] Focus chain FC [auth K] Focus chain GB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain MC [auth L] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth I] Focus chain XA [auth F] Focus chain Z [auth B] Focus chain ZB [auth J] Interactions & Density Focus chain FA [auth C] Focus chain FC [auth K] Focus chain GB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain MC [auth L] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth I] Focus chain XA [auth F] Focus chain Z [auth B] Focus chain ZB [auth J]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain EC [auth K] SDF format, chain FB [auth G] SDF format, chain LA [auth D] SDF format, chain LB [auth H] SDF format, chain LC [auth L] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain RB [auth I] SDF format, chain WA [auth F] SDF format, chain Y [auth B] SDF format, chain YB [auth J] MOL2 format, chain EA [auth C] MOL2 format, chain EC [auth K] MOL2 format, chain FB [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth H] MOL2 format, chain LC [auth L] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth I] MOL2 format, chain WA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth J] mmCIF format, chain EA [auth C] mmCIF format, chain EC [auth K] mmCIF format, chain FB [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth H] mmCIF format, chain LC [auth L] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth I] mmCIF format, chain WA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth J]	EA [auth C] EC [auth K] FB [auth G] LA [auth D] LB [auth H] EA [auth C], EC [auth K], FB [auth G], LA [auth D], LB [auth H], LC [auth L], R [auth A], RA [auth E], RB [auth I], WA [auth F], Y [auth B], YB [auth J]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain EC [auth K] Focus chain FB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain LC [auth L] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth I] Focus chain WA [auth F] Focus chain Y [auth B] Focus chain YB [auth J] Interactions & Density Focus chain EA [auth C] Focus chain EC [auth K] Focus chain FB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain LC [auth L] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth I] Focus chain WA [auth F] Focus chain Y [auth B] Focus chain YB [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain BC [auth K] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain CC [auth K] SDF format, chain DA [auth C] SDF format, chain DB [auth G] SDF format, chain DC [auth K] SDF format, chain EB [auth G] SDF format, chain HA [auth D] SDF format, chain HC [auth L] SDF format, chain IA [auth D] SDF format, chain IB [auth H] SDF format, chain IC [auth L] SDF format, chain JA [auth D] SDF format, chain JB [auth H] SDF format, chain JC [auth L] SDF format, chain KA [auth D] SDF format, chain KB [auth H] SDF format, chain KC [auth L] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain OB [auth I] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain QB [auth I] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain UB [auth J] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain VB [auth J] SDF format, chain W [auth B] SDF format, chain WB [auth J] SDF format, chain X [auth B] SDF format, chain XB [auth J] SDF format, chain ZA [auth G] SDF format, chain PB [auth I] SDF format, chain N [auth A] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth K] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain CC [auth K] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth K] MOL2 format, chain EB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain HC [auth L] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain IC [auth L] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain JC [auth L] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth H] MOL2 format, chain KC [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth I] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth I] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth J] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth J] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth J] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth J] MOL2 format, chain ZA [auth G] MOL2 format, chain PB [auth I] MOL2 format, chain N [auth A] mmCIF format, chain AB [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth K] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain CC [auth K] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth K] mmCIF format, chain EB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain HC [auth L] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain IC [auth L] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain JC [auth L] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth H] mmCIF format, chain KC [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain OB [auth I] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain QB [auth I] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain UB [auth J] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain VB [auth J] mmCIF format, chain W [auth B] mmCIF format, chain WB [auth J] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth J] mmCIF format, chain ZA [auth G] mmCIF format, chain PB [auth I] mmCIF format, chain N [auth A]	AB [auth G] BA [auth C] BB [auth G] BC [auth K] CA [auth C] AB [auth G], BA [auth C], BB [auth G], BC [auth K], CA [auth C], CB [auth G], CC [auth K], DA [auth C], DB [auth G], DC [auth K], EB [auth G], HA [auth D], HC [auth L], IA [auth D], IB [auth H], IC [auth L], JA [auth D], JB [auth H], JC [auth L], KA [auth D], KB [auth H], KC [auth L], M [auth A], N [auth A], O [auth A], OA [auth E], OB [auth I], P [auth A], PA [auth E], PB [auth I], Q [auth A], QA [auth E], QB [auth I], U [auth B], UA [auth F], UB [auth J], V [auth B], VA [auth F], VB [auth J], W [auth B], WB [auth J], X [auth B], XB [auth J], ZA [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain BC [auth K] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain CC [auth K] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain DC [auth K] Focus chain EB [auth G] Focus chain HA [auth D] Focus chain HC [auth L] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain IC [auth L] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain JC [auth L] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain KC [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth I] Focus chain P [auth A] Focus chain PA [auth E] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain QB [auth I] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth J] Focus chain W [auth B] Focus chain WB [auth J] Focus chain X [auth B] Focus chain XB [auth J] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain BC [auth K] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain CC [auth K] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain DC [auth K] Focus chain EB [auth G] Focus chain HA [auth D] Focus chain HC [auth L] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain IC [auth L] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain JC [auth L] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain KC [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth I] Focus chain P [auth A] Focus chain PA [auth E] Focus chain PB [auth I] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain QB [auth I] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth J] Focus chain W [auth B] Focus chain WB [auth J] Focus chain X [auth B] Focus chain XB [auth J] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.178 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

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
Version 2.1: 2024-03-13
Changes: Data collection, Database references, Structure summary