5JYD

Crystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb5JYD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-13 Released: 2016-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.174
R-Value Work: 0.141
R-Value Observed: 0.142

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

TBD

SSGCID, Yano, J.Y., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 273.68 kDa
Atom Count: 19,905
Modelled Residue Count: 2,330
Deposited Residue Count: 2,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	310	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL1205
UniProt
Find proteins for B4EEE3 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EEE3 Go to UniProtKB: B4EEE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EEE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain BC [auth H] SDF format, chain I [auth A] SDF format, chain KA [auth D] SDF format, chain RB [auth G] SDF format, chain BA [auth C] SDF format, chain IB [auth F] SDF format, chain S [auth B] SDF format, chain VA [auth E] MOL2 format, chain BC [auth H] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain RB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth E]	BA [auth C] BC [auth H] I [auth A] IB [auth F] KA [auth D] BA [auth C], BC [auth H], I [auth A], IB [auth F], KA [auth D], RB [auth G], S [auth B], VA [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth C] Focus chain BC [auth H] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain RB [auth G] Focus chain S [auth B] Focus chain VA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain BC [auth H] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain RB [auth G] Focus chain S [auth B] Focus chain VA [auth E]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain DA [auth C] SDF format, chain DC [auth H] SDF format, chain EA [auth C] SDF format, chain EB [auth E] SDF format, chain FC [auth H] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain IC [auth H] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NA [auth D] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PB [auth F] SDF format, chain Q [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TB [auth G] SDF format, chain U [auth B] SDF format, chain VB [auth G] SDF format, chain W [auth B] SDF format, chain WB [auth G] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EC [auth H] SDF format, chain FA [auth C] SDF format, chain GC [auth H] SDF format, chain HC [auth H] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain QB [auth F] SDF format, chain UB [auth G] SDF format, chain V [auth B] SDF format, chain XB [auth G] SDF format, chain Y [auth B] SDF format, chain YB [auth G] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain DC [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth E] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain IC [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TB [auth G] MOL2 format, chain U [auth B] MOL2 format, chain VB [auth G] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth G] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EC [auth H] MOL2 format, chain FA [auth C] MOL2 format, chain GC [auth H] MOL2 format, chain HC [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth F] MOL2 format, chain UB [auth G] MOL2 format, chain V [auth B] MOL2 format, chain XB [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth G] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E]	AA [auth B] AB [auth E] BB [auth E] CB [auth E] DA [auth C] AA [auth B], AB [auth E], BB [auth E], CB [auth E], DA [auth C], DB [auth E], DC [auth H], EA [auth C], EB [auth E], EC [auth H], FA [auth C], FC [auth H], GA [auth C], GC [auth H], HA [auth C], HC [auth H], IA [auth C], IC [auth H], K [auth A], KB [auth F], L [auth A], LB [auth F], M [auth A], MA [auth D], MB [auth F], N [auth A], NA [auth D], NB [auth F], O [auth A], OA [auth D], OB [auth F], P [auth A], PA [auth D], PB [auth F], Q [auth A], QA [auth D], QB [auth F], RA [auth D], SA [auth D], TB [auth G], U [auth B], UB [auth G], V [auth B], VB [auth G], W [auth B], WB [auth G], X [auth B], XA [auth E], XB [auth G], Y [auth B], YA [auth E], YB [auth G], Z [auth B], ZA [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain DC [auth H] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HC [auth H] Focus chain IA [auth C] Focus chain IC [auth H] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VB [auth G] Focus chain W [auth B] Focus chain WB [auth G] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth G] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain DC [auth H] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HC [auth H] Focus chain IA [auth C] Focus chain IC [auth H] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VB [auth G] Focus chain W [auth B] Focus chain WB [auth G] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth G] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain Z [auth B] Focus chain ZA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GB [auth E] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain ZB [auth G] SDF format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain ZB [auth G] MOL2 format, chain FB [auth E]	FB [auth E], GB [auth E], TA [auth D], UA [auth D], ZB [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth E] Focus chain GB [auth E] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain ZB [auth G] Interactions & Density Focus chain FB [auth E] Focus chain GB [auth E] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain ZB [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain JB [auth F] SDF format, chain LA [auth D] SDF format, chain SB [auth G] SDF format, chain T [auth B] SDF format, chain CA [auth C] SDF format, chain CC [auth H] SDF format, chain J [auth A] SDF format, chain WA [auth E] MOL2 format, chain JB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain SB [auth G] MOL2 format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain CC [auth H] MOL2 format, chain J [auth A] MOL2 format, chain WA [auth E]	CA [auth C] CC [auth H] J [auth A] JB [auth F] LA [auth D] CA [auth C], CC [auth H], J [auth A], JB [auth F], LA [auth D], SB [auth G], T [auth B], WA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain CC [auth H] Focus chain J [auth A] Focus chain JB [auth F] Focus chain LA [auth D] Focus chain SB [auth G] Focus chain T [auth B] Focus chain WA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain CC [auth H] Focus chain J [auth A] Focus chain JB [auth F] Focus chain LA [auth D] Focus chain SB [auth G] Focus chain T [auth B] Focus chain WA [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AC [auth G] SDF format, chain HB [auth E] SDF format, chain JA [auth C] SDF format, chain R [auth A] MOL2 format, chain AC [auth G] MOL2 format, chain HB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain R [auth A]	AC [auth G], HB [auth E], JA [auth C], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AC [auth G] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain R [auth A] Interactions & Density Focus chain AC [auth G] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain R [auth A]