2V4B | pdb_00002v4b

Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (apo-form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.263 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2V4B

This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of Human Adamts-1 Reveal a Conserved Catalytic Domain and a Disintegrin-Like Domain with a Fold Homologous to Cysteine-Rich Domains.

Gerhardt, S.Hassall, G.Hawtin, P.Mccall, E.Flavell, L.Minshull, C.Hargreaves, D.Ting, A.Pauptit, R.A.Parker, A.E.Abbott, W.M.

(2007) J Mol Biology 373: 891

  • DOI: https://doi.org/10.1016/j.jmb.2007.07.047
  • Primary Citation Related Structures: 
    2JIH, 2V4B

  • PubMed Abstract: 

    The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type I motifs) family of proteases plays a role in pathological conditions including arthritis, cancer, thrombotic thrombocytopenic purpura and the Ehlers-Danlos type VIIC and Weill-Marchesani genetic syndromes. Here, we report the first crystal structures for a member of the ADAMTS family, ADAMTS-1. Originally cloned as an inflammation-associated gene, ADAMTS-1 has been shown to be involved in tissue remodelling, wound healing and angiogenesis. The crystal structures contain catalytic and disintegrin-like domains, both in the inhibitor-free form and in complex with the inhibitor marimastat. The overall fold of the catalytic domain is similar to related zinc metalloproteinases such as matrix metalloproteinases and ADAMs (a disintegrin and metalloproteinases). The active site contains the expected organisation of residues to coordinate zinc but has a much larger S1' selectivity pocket than ADAM33. The structure also unexpectedly reveals a double calcium-binding site. Also surprisingly, the previously named disintegrin-like domain showed no structural homology to the disintegrin domains of other metalloproteinases such as ADAM10 but is instead very similar in structure to the cysteine-rich domains of other metalloproteinases. Thus, this study suggests that the D (for disintegrin-like) in the nomenclature of ADAMTS enzymes is likely to be a misnomer. The ADAMTS-1 cysteine-rich domain stacks against the active site, suggesting a possible regulatory role.


  • Organizational Affiliation
    • Global Structural Chemistry, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

Macromolecule Content 

  • Total Structure Weight: 67.39 kDa 
  • Atom Count: 4,556 
  • Modeled Residue Count: 561 
  • Deposited Residue Count: 600 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAMTS-1
A, B
300Homo sapiensMutation(s): 0 
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI8 (Homo sapiens)
Explore Q9UHI8 
Go to UniProtKB:  Q9UHI8
PHAROS:  Q9UHI8
GTEx:  ENSG00000154734 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHI8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
T [auth B],
V [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
S [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
AA [auth B]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
AA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
U [auth B],
W [auth B],
Y [auth B],
Z [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
K [auth A],
P [auth A],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BA [auth B],
CA [auth B],
Q [auth A],
R [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.263 (Depositor) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.579α = 90
b = 64.396β = 90.91
c = 113.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-04-24
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary