6ZZR | pdb_00006zzr

The Crystal Structure of human LDHA from Biortus.

PDB DOI: https://doi.org/10.2210/pdb6ZZR/pdb

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

Deposited: 2020-08-05 Released: 2020-08-19
Deposition Author(s): Wang, F., Lin, D., Cheng, W., Bao, X., Zhu, B., Shang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.277 (Depositor), 0.274 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of human LDHA from Biortus

Wang, F., Lin, D., Cheng, W., Bao, X., Zhu, B., Shang, H.

To be published.

Macromolecule Content

Total Structure Weight: 310.63 kDa
Atom Count: 20,943
Modeled Residue Count: 2,643
Deposited Residue Count: 2,784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH]	348	Homo sapiens	Mutation(s): 0 Gene Names: LDHA, PIG19 EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens) Explore P00338 Go to UniProtKB: P00338
PHAROS: P00338 GTEx: ENSG00000134333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00338
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth BBB] SDF format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain S [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain S [auth BBB]	S [auth BBB], T [auth BBB]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth BBB] Focus chain T [auth BBB] Interactions & Density Focus chain S [auth BBB] Focus chain T [auth BBB]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth EEE] SDF format, chain BA [auth EEE] SDF format, chain CA [auth FFF] SDF format, chain DA [auth FFF] SDF format, chain EA [auth FFF] SDF format, chain FA [auth GGG] SDF format, chain GA [auth GGG] SDF format, chain HA [auth HHH] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain O [auth AAA] SDF format, chain P [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain R [auth BBB] SDF format, chain U [auth CCC] SDF format, chain V [auth CCC] SDF format, chain W [auth DDD] SDF format, chain X [auth DDD] SDF format, chain Y [auth DDD] SDF format, chain Z [auth DDD] MOL2 format, chain AA [auth EEE] MOL2 format, chain BA [auth EEE] MOL2 format, chain CA [auth FFF] MOL2 format, chain DA [auth FFF] MOL2 format, chain EA [auth FFF] MOL2 format, chain FA [auth GGG] MOL2 format, chain GA [auth GGG] MOL2 format, chain HA [auth HHH] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain R [auth BBB] MOL2 format, chain U [auth CCC] MOL2 format, chain V [auth CCC] MOL2 format, chain W [auth DDD] MOL2 format, chain X [auth DDD] MOL2 format, chain Y [auth DDD] MOL2 format, chain Z [auth DDD] mmCIF format, chain AA [auth EEE] mmCIF format, chain BA [auth EEE] mmCIF format, chain CA [auth FFF] mmCIF format, chain DA [auth FFF] mmCIF format, chain EA [auth FFF] mmCIF format, chain FA [auth GGG] mmCIF format, chain GA [auth GGG] mmCIF format, chain HA [auth HHH] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain R [auth BBB] mmCIF format, chain U [auth CCC] mmCIF format, chain V [auth CCC] mmCIF format, chain W [auth DDD] mmCIF format, chain X [auth DDD] mmCIF format, chain Y [auth DDD] mmCIF format, chain Z [auth DDD]	AA [auth EEE] BA [auth EEE] CA [auth FFF] DA [auth FFF] EA [auth FFF] AA [auth EEE], BA [auth EEE], CA [auth FFF], DA [auth FFF], EA [auth FFF], FA [auth GGG], GA [auth GGG], HA [auth HHH], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], P [auth AAA], Q [auth AAA], R [auth BBB], U [auth CCC], V [auth CCC], W [auth DDD], X [auth DDD], Y [auth DDD], Z [auth DDD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth EEE] Focus chain BA [auth EEE] Focus chain CA [auth FFF] Focus chain DA [auth FFF] Focus chain EA [auth FFF] Focus chain FA [auth GGG] Focus chain GA [auth GGG] Focus chain HA [auth HHH] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth BBB] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth DDD] Focus chain X [auth DDD] Focus chain Y [auth DDD] Focus chain Z [auth DDD] Interactions & Density Focus chain AA [auth EEE] Focus chain BA [auth EEE] Focus chain CA [auth FFF] Focus chain DA [auth FFF] Focus chain EA [auth FFF] Focus chain FA [auth GGG] Focus chain GA [auth GGG] Focus chain HA [auth HHH] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth BBB] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth DDD] Focus chain X [auth DDD] Focus chain Y [auth DDD] Focus chain Z [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.277 (Depositor), 0.274 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.959	α = 90
b = 66.479	β = 100.097
c = 250.843	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-08-19
Type: Initial release
Version 1.1: 2022-02-23
Changes: Database references, Structure summary
Version 1.2: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-04-24
Changes: Structure summary