8TVT

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfurase403Homo sapiensMutation(s): 0 
Gene Names: NFS1NIFSHUSSY-08
EC: 2.8.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y697 (Homo sapiens)
Explore Q9Y697 
Go to UniProtKB:  Q9Y697
PHAROS:  Q9Y697
GTEx:  ENSG00000244005 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y697
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LYR motif-containing protein 491Homo sapiensMutation(s): 1 
Gene Names: LYRM4C6orf149ISD11CGI-203
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD34 (Homo sapiens)
Explore Q9HD34 
Go to UniProtKB:  Q9HD34
PHAROS:  Q9HD34
GTEx:  ENSG00000214113 
Entity Groups  
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UniProt GroupQ9HD34
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein76Escherichia coliMutation(s): 0 
Gene Names: acpP
UniProt
Find proteins for A7ZKJ7 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZKJ7 
Go to UniProtKB:  A7ZKJ7
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UniProt GroupA7ZKJ7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur cluster assembly enzyme ISCU135Homo sapiensMutation(s): 0 
Gene Names: ISCU
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens)
Explore Q9H1K1 
Go to UniProtKB:  Q9H1K1
PHAROS:  Q9H1K1
GTEx:  ENSG00000136003 
Entity Groups  
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UniProt GroupQ9H1K1
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8Q1
Query on 8Q1

Download Ideal Coordinates CCD File 
WA [auth C]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
P15
Query on P15

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Y [auth A]2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
C13 H28 O7
FHHGCKHKTAJLOM-UHFFFAOYSA-N
EDT
Query on EDT

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UA [auth B]{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
PLP (Subject of Investigation/LOI)
Query on PLP

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G [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
1PE
Query on 1PE

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BB [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MES
Query on MES

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XA [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4
Query on PG4

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U [auth A],
V [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
DTT
Query on DTT

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CA [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
PGE
Query on PGE

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HA [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
LPH (Subject of Investigation/LOI)
Query on LPH

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H [auth A]L-Propargylglycine
C5 H7 N O2
DGYHPLMPMRKMPD-BYPYZUCNSA-N
PEG
Query on PEG

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BA [auth A]
LA [auth A]
MA [auth A]
PA [auth B]
RA [auth B]
BA [auth A],
LA [auth A],
MA [auth A],
PA [auth B],
RA [auth B],
T [auth A],
W [auth A],
Z [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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CB [auth D],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth A]
AB [auth D]
DA [auth A]
DB [auth D]
E [auth A]
AA [auth A],
AB [auth D],
DA [auth A],
DB [auth D],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
GA [auth A],
IA [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
M [auth A],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
Q [auth A],
QA [auth B],
R [auth A],
S [auth A],
SA [auth B],
TA [auth B],
VA [auth B],
X [auth A],
YA [auth C],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.27α = 90
b = 86.27β = 90
c = 246.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AutoProcessdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release