8S88 | pdb_00008s88

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

PDB DOI: https://doi.org/10.2210/pdb8S88/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-06 Released: 2025-03-19
Deposition Author(s): Van Gysel, M., Wouters, J.
Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.264 (Depositor), 0.265 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

Van Gysel, M., Wouters, J.

To be published.

Macromolecule Content

Total Structure Weight: 478.73 kDa
Atom Count: 33,118
Modeled Residue Count: 3,998
Deposited Residue Count: 4,188
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase B chain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	349	Homo sapiens	Mutation(s): 0 Gene Names: LDHB EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P07195 (Homo sapiens) Explore P07195 Go to UniProtKB: P07195
PHAROS: P07195 GTEx: ENSG00000111716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07195
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download:Ideal Coordinates CCD File SDF format, chain AC [auth L] SDF format, chain BA [auth C] SDF format, chain DB [auth H] SDF format, chain HA [auth D] SDF format, chain LB [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain VB [auth K] SDF format, chain XA [auth G] SDF format, chain OB [auth J] MOL2 format, chain AC [auth L] MOL2 format, chain BA [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain LB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain XA [auth G] MOL2 format, chain OB [auth J] mmCIF format, chain AC [auth L] mmCIF format, chain BA [auth C] mmCIF format, chain DB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain LB [auth I] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain VB [auth K] mmCIF format, chain XA [auth G] mmCIF format, chain OB [auth J]	AC [auth L] BA [auth C] DB [auth H] HA [auth D] LB [auth I] AC [auth L], BA [auth C], DB [auth H], HA [auth D], LB [auth I], O [auth A], OA [auth E], OB [auth J], SA [auth F], T [auth B], VB [auth K], XA [auth G]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain AC [auth L] Focus chain BA [auth C] Focus chain DB [auth H] Focus chain HA [auth D] Focus chain LB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain SA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain XA [auth G] Interactions & Density Focus chain AC [auth L] Focus chain BA [auth C] Focus chain DB [auth H] Focus chain HA [auth D] Focus chain LB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth J] Focus chain SA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain XA [auth G]
SFX (Subject of Investigation/LOI) Query on SFX Download:Ideal Coordinates CCD File SDF format, chain JB [auth I] SDF format, chain M [auth A] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain JB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain JB [auth I] mmCIF format, chain M [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	JB [auth I], M [auth A], QA [auth F], R [auth B], Z [auth C]	(3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine C₁₇ H₁₈ F₃ N O RTHCYVBBDHJXIQ-INIZCTEOSA-N		Interactions Focus chain JB [auth I] Focus chain M [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain JB [auth I] Focus chain M [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain Z [auth C]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain BC [auth L] SDF format, chain CA [auth C] SDF format, chain P [auth A] SDF format, chain TA [auth F] SDF format, chain WB [auth K] SDF format, chain YA [auth G] MOL2 format, chain BC [auth L] MOL2 format, chain CA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth F] MOL2 format, chain WB [auth K] MOL2 format, chain YA [auth G] mmCIF format, chain BC [auth L] mmCIF format, chain CA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain TA [auth F] mmCIF format, chain WB [auth K] mmCIF format, chain YA [auth G]	BC [auth L] CA [auth C] P [auth A] TA [auth F] WB [auth K] BC [auth L], CA [auth C], P [auth A], TA [auth F], WB [auth K], YA [auth G]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain BC [auth L] Focus chain CA [auth C] Focus chain P [auth A] Focus chain TA [auth F] Focus chain WB [auth K] Focus chain YA [auth G] Interactions & Density Focus chain BC [auth L] Focus chain CA [auth C] Focus chain P [auth A] Focus chain TA [auth F] Focus chain WB [auth K] Focus chain YA [auth G]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain IB [auth H] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain SB [auth J] SDF format, chain TB [auth J] SDF format, chain Y [auth B] SDF format, chain PA [auth E] MOL2 format, chain IB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain SB [auth J] MOL2 format, chain TB [auth J] MOL2 format, chain Y [auth B] MOL2 format, chain PA [auth E] mmCIF format, chain IB [auth H] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain SB [auth J] mmCIF format, chain TB [auth J] mmCIF format, chain Y [auth B] mmCIF format, chain PA [auth E]	IB [auth H] LA [auth D] MA [auth D] PA [auth E] SB [auth J] IB [auth H], LA [auth D], MA [auth D], PA [auth E], SB [auth J], TB [auth J], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain IB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain PA [auth E] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain Y [auth B] Interactions & Density Focus chain IB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain PA [auth E] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain Y [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain FC [auth L] SDF format, chain GC [auth L] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain Q [auth A] SDF format, chain QB [auth J] SDF format, chain RB [auth J] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth L] MOL2 format, chain GC [auth L] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth J] MOL2 format, chain RB [auth J] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain BB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth L] mmCIF format, chain GC [auth L] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth J] mmCIF format, chain RB [auth J] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	BB [auth G] EA [auth C] FA [auth C] FC [auth L] GC [auth L] BB [auth G], EA [auth C], FA [auth C], FC [auth L], GC [auth L], JA [auth D], KA [auth D], Q [auth A], QB [auth J], RB [auth J], W [auth B], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BB [auth G] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FC [auth L] Focus chain GC [auth L] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BB [auth G] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FC [auth L] Focus chain GC [auth L] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain W [auth B] Focus chain X [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain CC [auth L] SDF format, chain DA [auth C] SDF format, chain DC [auth L] SDF format, chain EB [auth H] SDF format, chain EC [auth L] SDF format, chain FB [auth H] SDF format, chain GB [auth H] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain MB [auth I] SDF format, chain PB [auth J] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain XB [auth K] SDF format, chain YB [auth K] SDF format, chain ZA [auth G] SDF format, chain U [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain CC [auth L] MOL2 format, chain DA [auth C] MOL2 format, chain DC [auth L] MOL2 format, chain EB [auth H] MOL2 format, chain EC [auth L] MOL2 format, chain FB [auth H] MOL2 format, chain GB [auth H] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain MB [auth I] MOL2 format, chain PB [auth J] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain XB [auth K] MOL2 format, chain YB [auth K] MOL2 format, chain ZA [auth G] MOL2 format, chain U [auth B] mmCIF format, chain AB [auth G] mmCIF format, chain CC [auth L] mmCIF format, chain DA [auth C] mmCIF format, chain DC [auth L] mmCIF format, chain EB [auth H] mmCIF format, chain EC [auth L] mmCIF format, chain FB [auth H] mmCIF format, chain GB [auth H] mmCIF format, chain HB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain MB [auth I] mmCIF format, chain PB [auth J] mmCIF format, chain UA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain XB [auth K] mmCIF format, chain YB [auth K] mmCIF format, chain ZA [auth G] mmCIF format, chain U [auth B]	AB [auth G] CC [auth L] DA [auth C] DC [auth L] EB [auth H] AB [auth G], CC [auth L], DA [auth C], DC [auth L], EB [auth H], EC [auth L], FB [auth H], GB [auth H], HB [auth H], IA [auth D], MB [auth I], PB [auth J], U [auth B], UA [auth F], V [auth B], VA [auth F], XB [auth K], YB [auth K], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain CC [auth L] Focus chain DA [auth C] Focus chain DC [auth L] Focus chain EB [auth H] Focus chain EC [auth L] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain MB [auth I] Focus chain PB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain XB [auth K] Focus chain YB [auth K] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain CC [auth L] Focus chain DA [auth C] Focus chain DC [auth L] Focus chain EB [auth H] Focus chain EC [auth L] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain MB [auth I] Focus chain PB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain XB [auth K] Focus chain YB [auth K] Focus chain ZA [auth G]
OXM (Subject of Investigation/LOI) Query on OXM Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CB [auth H] SDF format, chain GA [auth D] SDF format, chain KB [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain NB [auth J] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain WA [auth G] SDF format, chain ZB [auth L] SDF format, chain UB [auth K] MOL2 format, chain AA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth J] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth G] MOL2 format, chain ZB [auth L] MOL2 format, chain UB [auth K] mmCIF format, chain AA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain KB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain NB [auth J] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth G] mmCIF format, chain ZB [auth L] mmCIF format, chain UB [auth K]	AA [auth C] CB [auth H] GA [auth D] KB [auth I] N [auth A] AA [auth C], CB [auth H], GA [auth D], KB [auth I], N [auth A], NA [auth E], NB [auth J], RA [auth F], S [auth B], UB [auth K], WA [auth G], ZB [auth L]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CB [auth H] Focus chain GA [auth D] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain RA [auth F] Focus chain S [auth B] Focus chain UB [auth K] Focus chain WA [auth G] Focus chain ZB [auth L] Interactions & Density Focus chain AA [auth C] Focus chain CB [auth H] Focus chain GA [auth D] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth J] Focus chain RA [auth F] Focus chain S [auth B] Focus chain UB [auth K] Focus chain WA [auth G] Focus chain ZB [auth L]