9DQ9 | pdb_00009dq9

Borrelia burgdorferi LDH with NADH and oxamate

PDB DOI: https://doi.org/10.2210/pdb9DQ9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Borreliella burgdorferi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-23 Released: 2025-03-12
Deposition Author(s): Lynch, M.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.200 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Borrelia burgdorferi LDH with NADH and oxamate

Lynch, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 141.65 kDa
Atom Count: 10,083
Modeled Residue Count: 1,256
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A [auth P], B [auth A], C [auth B], D [auth C]	314	Borreliella burgdorferi	Mutation(s): 0 Gene Names: ldh, BB_0087 EC: 1.1.1.27
UniProt
Find proteins for O51114 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O51114 Go to UniProtKB: O51114
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O51114
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6V0 Query on 6V0 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain E [auth P] MOL2 format, chain H [auth A] MOL2 format, chain E [auth P] mmCIF format, chain H [auth A] mmCIF format, chain E [auth P]	E [auth P], H [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C₂₁ H₂₉ N₇ O₁₄ P₂ QVQHBKNZCMZBKP-NNYOXOHSSA-N		Interactions Focus chain E [auth P] Focus chain H [auth A] Interactions & Density Focus chain E [auth P] Focus chain H [auth A]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B]	L [auth B], O [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain L [auth B] Focus chain O [auth C]
OXM Query on OXM Download Ideal Coordinates CCD File SDF format, chain F [auth P] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth P] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth P] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	F [auth P], I [auth A], M [auth B], P [auth C]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain F [auth P] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth P] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth P] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth P] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth P]	G [auth P], J [auth A], K [auth A], N [auth B], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth P] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth P] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.200 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.528	α = 90
b = 90.348	β = 90
c = 167.361	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Lynch, M.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01AI148844
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI078958
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DE023080