8UGO | pdb_00008ugo

Structure of the complex between Human LIAS and H-protein in the presence of 5'-deoxyadenosine

PDB DOI: https://doi.org/10.2210/pdb8UGO/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia
Mutation(s): No

Deposited: 2023-10-05 Released: 2025-07-09
Deposition Author(s): Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.186 (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

Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein

Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 185.71 kDa
Atom Count: 10,316
Modeled Residue Count: 1,265
Deposited Residue Count: 1,623
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoyl synthase, mitochondrial	A, C [auth B], E [auth D]	368	Homo sapiens	Mutation(s): 0 Gene Names: LIAS, LAS, HUSSY-01 EC: 2.8.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for O43766 (Homo sapiens) Explore O43766 Go to UniProtKB: O43766
PHAROS: O43766 GTEx: ENSG00000121897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43766
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine cleavage system H protein, mitochondrial	B [auth E], D [auth C], F	173	Homo sapiens	Mutation(s): 0 Gene Names: GCSH
UniProt & NIH Common Fund Data Resources
Find proteins for P23434 (Homo sapiens) Explore P23434 Go to UniProtKB: P23434
PHAROS: P23434 GTEx: ENSG00000140905
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23434
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth D]	H [auth A], O [auth B], V [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth D]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth D]	I [auth A], P [auth B], X [auth D]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth D]
5AD (Subject of Investigation/LOI) Query on 5AD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain W [auth D]	G [auth A], N [auth B], W [auth D]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
YVI (Subject of Investigation/LOI) Query on YVI Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain U [auth C] SDF format, chain Z [auth F] MOL2 format, chain M [auth E] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth F] mmCIF format, chain M [auth E] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth F]	M [auth E], U [auth C], Z [auth F]	6-THIOOCTANOIC ACID C₈ H₁₆ O₂ S LABZAONVGARYLS-ZETCQYMHSA-N		Interactions Focus chain M [auth E] Focus chain U [auth C] Focus chain Z [auth F] Interactions & Density Focus chain M [auth E] Focus chain U [auth C] Focus chain Z [auth F]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
MET Query on MET Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth D] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth D]	L [auth A], S [auth B], Y [auth D]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth D] Interactions & Density Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.681	α = 90
b = 169.209	β = 90
c = 183.183	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-122595
National Science Foundation (NSF, United States)	United States	MCB1716686
Howard Hughes Medical Institute (HHMI)	United States	SJB