1E51

Crystal structure of native human erythrocyte 5-aminolaevulinic acid dehydratase

PDB DOI: https://doi.org/10.2210/pdb1E51/pdb

Classification: LYASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2000-07-13 Released: 2001-07-12
Deposition Author(s): Mills-Davies, N.L., Thompson, D., Cooper, J.B., Shoolingin-Jordan, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.270
R-Value Work: 0.213
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of Human Ala-Dehydratase

Mills-Davies, N.L., Thompson, D., Cooper, J.B., Wood, S.P., Shoolingin-Jordan, P.M.

To be published.

Macromolecule Content

Total Structure Weight: 73.16 kDa
Atom Count: 4,707
Modelled Residue Count: 625
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA-AMINOLEVULINIC ACID DEHYDRATASE	A, B	330	Homo sapiens	Mutation(s): 0 EC: 4.2.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for P13716 (Homo sapiens) Explore P13716 Go to UniProtKB: P13716
PHAROS: P13716 GTEx: ENSG00000148218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13716
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PBG Query on PBG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID C₁₀ H₁₄ N₂ O₄ QSHWIQZFGQKFMA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.270
R-Value Work: 0.213
R-Value Observed: 0.213
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.53	α = 90
b = 125.53	β = 90
c = 200.91	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing
CCP4	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-07-12

Deposition Author(s):

Mills-Davies, N.L.

Thompson, D.

Cooper, J.B.

Shoolingin-Jordan, P.M.

Revision History (Full details and data files)

Version 1.0: 2001-07-12
Type: Initial release
Version 1.1: 2014-02-05
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2018-04-18
Changes: Data collection, Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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1E51

Crystal structure of native human erythrocyte 5-aminolaevulinic acid dehydratase

The Crystal Structure of Human Ala-Dehydratase

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)