3N7U | pdb_00003n7u

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

PDB DOI: https://doi.org/10.2210/pdb3N7U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-27 Released: 2010-06-09
Deposition Author(s): Shabalin, I.G., Polyakov, K.M., Serov, A.E., Skirgello, O.E., Sadykhov, E.G., Dorovatovskiy, P.V., Tishkov, V.I., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.189 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana

Shabalin, I.G., Polyakov, K.M., Skirgello, O.E., Tishkov, V.I., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 478.97 kDa
Atom Count: 37,338
Modeled Residue Count: 4,212
Deposited Residue Count: 4,212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	351	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At5g14780, FDH, FDH1, T9L3_80 EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for Q9S7E4 (Arabidopsis thaliana) Explore Q9S7E4 Go to UniProtKB: Q9S7E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S7E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain IA [auth F] SDF format, chain JB [auth L] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain T [auth C] SDF format, chain VA [auth I] SDF format, chain Y [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JB [auth L] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain Y [auth D] mmCIF format, chain BB [auth J] mmCIF format, chain DB [auth K] mmCIF format, chain FA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JB [auth L] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain VA [auth I] mmCIF format, chain Y [auth D]	BB [auth J] DB [auth K] FA [auth E] IA [auth F] JB [auth L] BB [auth J], DB [auth K], FA [auth E], IA [auth F], JB [auth L], M [auth A], MA [auth G], P [auth B], QA [auth H], T [auth C], VA [auth I], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BB [auth J] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JB [auth L] Focus chain M [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain VA [auth I] Focus chain Y [auth D] Interactions & Density Focus chain BB [auth J] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain IA [auth F] Focus chain JB [auth L] Focus chain M [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain VA [auth I] Focus chain Y [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain KA [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain R [auth B] SDF format, chain SA [auth H] SDF format, chain V [auth C] SDF format, chain XA [auth I] SDF format, chain FB [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain XA [auth I] MOL2 format, chain FB [auth K] mmCIF format, chain AA [auth D] mmCIF format, chain KA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain XA [auth I] mmCIF format, chain FB [auth K]	AA [auth D] FB [auth K] KA [auth F] O [auth A] OA [auth G] AA [auth D], FB [auth K], KA [auth F], O [auth A], OA [auth G], R [auth B], SA [auth H], V [auth C], XA [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain FB [auth K] Focus chain KA [auth F] Focus chain O [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain XA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain FB [auth K] Focus chain KA [auth F] Focus chain O [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain XA [auth I]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain GB [auth K] SDF format, chain HA [auth E] SDF format, chain HB [auth K] SDF format, chain IB [auth K] SDF format, chain LA [auth F] SDF format, chain LB [auth L] SDF format, chain PA [auth G] SDF format, chain S [auth B] SDF format, chain TA [auth H] SDF format, chain UA [auth H] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain YA [auth I] SDF format, chain ZA [auth I] SDF format, chain AB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain GB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth K] MOL2 format, chain IB [auth K] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth L] MOL2 format, chain PA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth I] MOL2 format, chain AB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain GB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth K] mmCIF format, chain IB [auth K] mmCIF format, chain LA [auth F] mmCIF format, chain LB [auth L] mmCIF format, chain PA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain YA [auth I] mmCIF format, chain ZA [auth I] mmCIF format, chain AB [auth I]	AB [auth I] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AB [auth I], BA [auth D], CA [auth D], DA [auth D], EA [auth D], GB [auth K], HA [auth E], HB [auth K], IB [auth K], LA [auth F], LB [auth L], PA [auth G], S [auth B], TA [auth H], UA [auth H], W [auth C], X [auth C], YA [auth I], ZA [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain LA [auth F] Focus chain LB [auth L] Focus chain PA [auth G] Focus chain S [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth I] Focus chain ZA [auth I] Interactions & Density Focus chain AB [auth I] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain LA [auth F] Focus chain LB [auth L] Focus chain PA [auth G] Focus chain S [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth I] Focus chain ZA [auth I]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain CB [auth J] SDF format, chain EB [auth K] SDF format, chain GA [auth E] SDF format, chain JA [auth F] SDF format, chain KB [auth L] SDF format, chain N [auth A] SDF format, chain RA [auth H] SDF format, chain U [auth C] SDF format, chain WA [auth I] SDF format, chain Z [auth D] SDF format, chain Q [auth B] SDF format, chain NA [auth G] MOL2 format, chain CB [auth J] MOL2 format, chain EB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KB [auth L] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain WA [auth I] MOL2 format, chain Z [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth G] mmCIF format, chain CB [auth J] mmCIF format, chain EB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain KB [auth L] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain WA [auth I] mmCIF format, chain Z [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth G]	CB [auth J] EB [auth K] GA [auth E] JA [auth F] KB [auth L] CB [auth J], EB [auth K], GA [auth E], JA [auth F], KB [auth L], N [auth A], NA [auth G], Q [auth B], RA [auth H], U [auth C], WA [auth I], Z [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain CB [auth J] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain JA [auth F] Focus chain KB [auth L] Focus chain N [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain WA [auth I] Focus chain Z [auth D] Interactions & Density Focus chain CB [auth J] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain JA [auth F] Focus chain KB [auth L] Focus chain N [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain WA [auth I] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.189 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.62	α = 90
b = 217.68	β = 92.62
c = 139.11	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-06-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations