6P6U | pdb_00006p6u

Crystal Structure of Monoclinic Rabbit Muscle Lactate Dehydrogenase with Four Tetramers as the Asymmetric Unit

PDB DOI: https://doi.org/10.2210/pdb6P6U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryctolagus cuniculus
Expression System: Oryctolagus cuniculus
Mutation(s): No

Deposited: 2019-06-04 Released: 2020-06-17
Deposition Author(s): McPherson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Monoclinic Rabbit Muscle Lactate Dehydrogenase with Four Tetramers as the Asymmetric Unit

McPherson, A.

To be published.

Macromolecule Content

Total Structure Weight: 586.5 kDa
Atom Count: 42,467
Modeled Residue Count: 5,296
Deposited Residue Count: 5,312
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	332	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: LDHA EC: 1.1.1.27
UniProt
Find proteins for P13491 (Oryctolagus cuniculus) Explore P13491 Go to UniProtKB: P13491
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain Q [auth C] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth C] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth C]	Q [auth C], R [auth E]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain Q [auth C] Focus chain R [auth E] Interactions & Density Focus chain Q [auth C] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.572	α = 90
b = 100.838	β = 101.23
c = 223.102	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.