2CLP | pdb_00002clp

Crystal structure of human aflatoxin B1 aldehyde reductase member 3

PDB DOI: https://doi.org/10.2210/pdb2CLP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-04-28 Released: 2006-05-12
Deposition Author(s): Debreczeni, J.E., Marsden, B.D., Johansson, C., Kavanagh, K., Guo, K., Smee, C., Gileadi, O., Turnbull, A., Papagrigoriou, E., von Delft, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.239 (Depositor), 0.243 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Human Aflatoxin B1 Aldehyde Reductase Member 3

Debreczeni, J.E., Johansson, C., Kavanagh, K., Turnbull, A., Papagrigoriou, E., von Delft, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 437.93 kDa
Atom Count: 27,441
Modeled Residue Count: 3,552
Deposited Residue Count: 3,817
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K	347	Homo sapiens	Mutation(s): 1 EC: 1.1.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O95154 (Homo sapiens) Explore O95154 Go to UniProtKB: O95154
PHAROS: O95154 GTEx: ENSG00000162482
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95154
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth E] SDF format, chain Z [auth K] SDF format, chain Y [auth J] SDF format, chain X [auth I] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth E] MOL2 format, chain Z [auth K] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth I] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth E] mmCIF format, chain Z [auth K] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth I] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth A]	L [auth A] N [auth B] O [auth C] Q [auth D] R [auth E] L [auth A], N [auth B], O [auth C], Q [auth D], R [auth E], T [auth F], U [auth G], W [auth H], X [auth I], Y [auth J], Z [auth K]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K] Interactions & Density Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth G] SDF format, chain S [auth E] SDF format, chain P [auth C] MOL2 format, chain M [auth A] MOL2 format, chain V [auth G] MOL2 format, chain S [auth E] MOL2 format, chain P [auth C] mmCIF format, chain M [auth A] mmCIF format, chain V [auth G] mmCIF format, chain S [auth E] mmCIF format, chain P [auth C]	M [auth A], P [auth C], S [auth E], V [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth C] Focus chain S [auth E] Focus chain V [auth G] Interactions & Density Focus chain M [auth A] Focus chain P [auth C] Focus chain S [auth E] Focus chain V [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.253 (Depositor), 0.255 (DCC)
R-Value Work: 0.239 (Depositor), 0.243 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.963	α = 90
b = 126.963	β = 90
c = 490.497	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2013-12-04
Changes: Database references, Derived calculations, Other, Source and taxonomy
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description