OCA Atlas for 3HDB

3HDB

Hydrolase

date

May 07, 2009

title

Crystal Structure Of Aahiv, A Metalloproteinase From Venom O Agkistrodon Acutus

authors

Z.Q.Zhu, L.W.Niu, M.K.Teng

compound

source

Molecule: Aahiv
Chain: A
Synonym: Zinc Metalloproteinase
Ec: 3.4.24.-

Organism_scientific: Agkistrodon Acutus
Organism_common: Hundred-Pace Snake
Organism_taxid: 36307

Molecule: Knl
Chain: L

Organism_scientific: Agkistrodon Acutus
Organism_common: Hundred-Pace Snake
Organism_taxid: 36307

symmetry

Space Group: C 2 2 21

R_factor

0.212

R_Free

0.249

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
111.190	122.278	94.721	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.31 Å

ligand

2PE, CA, CL, NAG, ZN

enzyme

Hydrolase E.C.3.4.24 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A

Primary reference

Structural basis of the autolysis of AaHIV suggests a novel target recognizing model for ADAM/reprolysin family proteins., Zhu Z, Gao Y, Zhu Z, Yu Y, Zhang X, Zang J, Teng M, Niu L, Biochem Biophys Res Commun. 2009 Aug 14;386(1):159-64. Epub 2009 Jun 6. PMID:19505434

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]

Biological Unit Coordinates (3hdb.pdb1.gz) 72 Kb

Biological Unit Coordinates (3hdb.pdb2.gz) 141 Kb

Biological Unit Coordinates (3hdb.pdb3.gz) 72 Kb

LPC: Ligand-Protein Contacts for 3HDB

CSU: Contacts of Structural Units for 3HDB

Structure Factors (468 Kb)

Retrieve 3HDB in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3HDB from S2C, [Save to disk]

Re-refined 3hdb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3HDB in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3HDB

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3HDB, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3hdb] [3hdb_L] [3hdb_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3HDB: [ACR] [DISIN ] by SMART

Other resources with information on 3HDB

Community annotation for 3HDB at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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