6W1D

Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis

Freibert, S.A.Boniecki, M.T.Shulz, V.Wilbrecht, C.Krapoth, N.Muhlenhoff, U.Stehling, O.Cygler, M.Lill, R.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfurase, mitochondrial406Homo 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
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HD34
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein77Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Explore P0A6A8 
Go to UniProtKB:  P0A6A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6A8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial143Homo sapiensMutation(s): 0 
Gene Names: ISCUNIFUN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1K1 (Homo sapiens)
Explore Q9H1K1 
Go to UniProtKB:  Q9H1K1
GTEx:  ENSG00000136003 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1K1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8Q1
Query on 8Q1

Download Ideal Coordinates CCD File 
RB [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

Download Ideal Coordinates CCD File 
DA [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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NB [auth B]{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
PLP
Query on PLP

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

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

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

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

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

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LA [auth A],
UA [auth A],
VA [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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AB [auth A]
BB [auth A]
EA [auth A]
IA [auth A]
JA [auth A]
AB [auth A],
BB [auth A],
EA [auth A],
IA [auth A],
JA [auth A],
JB [auth B],
LB [auth B],
V [auth A],
VB [auth C],
Y [auth A],
ZA [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth D]
CB [auth A]
F [auth A]
G [auth A]
H [auth A]
AC [auth D],
CB [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
BC [auth D]
CA [auth A]
CC [auth D]
AA [auth A],
BA [auth A],
BC [auth D],
CA [auth A],
CC [auth D],
DB [auth A],
EB [auth A],
FA [auth A],
FB [auth A],
GA [auth A],
GB [auth B],
HA [auth A],
HB [auth B],
IB [auth B],
J [auth A],
K [auth A],
KB [auth B],
L [auth A],
M [auth A],
MA [auth A],
MB [auth B],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
OB [auth B],
P [auth A],
PA [auth A],
PB [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
TA [auth A],
TB [auth C],
U [auth A],
UB [auth C],
WA [auth A],
WB [auth C],
XA [auth A],
XB [auth D],
YA [auth A],
Z [auth A],
ZB [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.348α = 90
b = 86.348β = 90
c = 245.359γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description