3S2E | pdb_00003s2e

Crystal Structure of FurX NADH Complex 1

PDB DOI: https://doi.org/10.2210/pdb3S2E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-16 Released: 2012-06-13
Deposition Author(s): Hayes, R., Sanchez, E.J., Webb, B.N., Hooper, T., Nissen, M.S., Li, Q., Xun, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.194 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.160 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structures and furfural reduction mechanism of a bacterial zinc-dependent alcohol dehydrogenase

Hayes, R., Sanchez, E.J., Webb, B.N., Hooper, T., Nissen, M.S., Li, Q., Xun, L.

To be published.

Macromolecule Content

Total Structure Weight: 292.06 kDa
Atom Count: 22,822
Modeled Residue Count: 2,720
Deposited Residue Count: 2,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-containing alcohol dehydrogenase superfamily	A, B, C, D, E A, B, C, D, E, F, G, H	340	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: Reut_B3677 EC: 1.1.1.1
UniProt
Find proteins for Q46UZ9 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46UZ9 Go to UniProtKB: Q46UZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46UZ9
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 JA [auth E] SDF format, chain NA [auth F] SDF format, chain QA [auth G] SDF format, chain XA [auth H] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain XA [auth H] mmCIF format, chain JA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain QA [auth G] mmCIF format, chain XA [auth H]	JA [auth E], NA [auth F], QA [auth G], XA [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain JA [auth E] Focus chain NA [auth F] Focus chain QA [auth G] Focus chain XA [auth H] Interactions & Density Focus chain JA [auth E] Focus chain NA [auth F] Focus chain QA [auth G] Focus chain XA [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain TA [auth G] SDF format, chain U [auth B] SDF format, chain UA [auth G] SDF format, chain V [auth B] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H]	BA [auth C] CA [auth C] HA [auth D] IA [auth D] MA [auth E] BA [auth C], CA [auth C], HA [auth D], IA [auth D], MA [auth E], N [auth A], O [auth A], TA [auth G], U [auth B], UA [auth G], V [auth B], YA [auth H], ZA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain YA [auth H] Focus chain ZA [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] FA [auth D] GA [auth D] K [auth A] L [auth A] AA [auth C], FA [auth D], GA [auth D], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B], T [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain RA [auth G] SDF format, chain SA [auth G] SDF format, chain VA [auth H] SDF format, chain W [auth C] SDF format, chain WA [auth H] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain SA [auth G] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth C]	DA [auth D] EA [auth D] I [auth A] J [auth A] KA [auth E] DA [auth D], EA [auth D], I [auth A], J [auth A], KA [auth E], LA [auth E], OA [auth F], P [auth B], PA [auth F], Q [auth B], RA [auth G], SA [auth G], VA [auth H], W [auth C], WA [auth H], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.194 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.160 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.187	α = 106.11
b = 92.744	β = 89.95
c = 117.684	γ = 90.13

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations