3P1M | pdb_00003p1m

Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster

PDB DOI: https://doi.org/10.2210/pdb3P1M/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-30 Released: 2010-11-03
Deposition Author(s): Chaikuad, A., Johansson, C., Krojer, T., Yue, W.W., Phillips, C., Bray, J.E., Pike, A.C.W., Muniz, J.R.C., Vollmar, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Kavanagh, K., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.241 (Depositor), 0.238 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster

Chaikuad, A., Johansson, C., Krojer, T., Yue, W.W., Phillips, C., Bray, J.E., Pike, A.C.W., Muniz, J.R.C., Vollmar, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Kavanagh, K., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 120.18 kDa
Atom Count: 8,161
Modeled Residue Count: 1,017
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adrenodoxin, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H	132	Homo sapiens	Mutation(s): 0 Gene Names: ADX, FDX1
UniProt & NIH Common Fund Data Resources
Find proteins for P10109 (Homo sapiens) Explore P10109 Go to UniProtKB: P10109
PHAROS: P10109 GTEx: ENSG00000137714
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10109
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain HA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain DA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	DA [auth G] HA [auth H] J [auth A] M [auth B] P [auth C] DA [auth G], HA [auth H], J [auth A], M [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], X [auth E]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] GA [auth H] I [auth A] L [auth B] O [auth C] CA [auth G], GA [auth H], I [auth A], L [auth B], O [auth C], S [auth D], W [auth E], Z [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth G]	BA [auth F], FA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain IA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	AA [auth F] EA [auth G] IA [auth H] K [auth A] N [auth B] AA [auth F], EA [auth G], IA [auth H], K [auth A], N [auth B], R [auth C], V [auth D], Y [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.241 (Depositor), 0.238 (DCC)
R-Value Work: 0.204 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.576	α = 90
b = 76.576	β = 90
c = 234.41	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-11-03

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description