4B7U | pdb_00004b7u

PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH BICINE

PDB DOI: https://doi.org/10.2210/pdb4B7U/pdb
Entry: 4B7U supersedes: 2YDN

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-08-22 Released: 2012-10-10
Deposition Author(s): Birkinshaw, R.W., Brady, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.176 (Depositor), 0.170 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of Plasmodium Falciparum L- Lactate Dehydrogenase in Complex with a Novel Bicine Ligand

Birkinshaw, R.W., Brady, R.L.

To be published.

Macromolecule Content

Total Structure Weight: 141.68 kDa
Atom Count: 10,481
Modeled Residue Count: 1,232
Deposited Residue Count: 1,288
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, B, C, D	322	Plasmodium falciparum	Mutation(s): 0 EC: 1.1.1.27
UniProt
Find proteins for Q71T02 (Plasmodium falciparum) Explore Q71T02 Go to UniProtKB: Q71T02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q71T02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A] K [auth B] L [auth B] M [auth B] O [auth C] F [auth A], K [auth B], L [auth B], M [auth B], O [auth C], Q [auth D], R [auth D], S [auth D]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain T [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain T [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], N [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.176 (Depositor), 0.170 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.29	α = 90
b = 154.779	β = 90
c = 58.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Birkinshaw, R.W.

Brady, R.L.

This entry supersedes: 2YDN

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description