6EVM Hydrolase date Nov 02, 2017
title Crystal Structure Of A Pro-9 Complexed Peptide-Substrate-Bin Domain Of Human Type II Collagen Prolyl 4-Hydroxylase
authors A.V.Murthy, R.Sulu, M.K.Koski, R.K.Wierenga
compound source
Molecule: Prolyl 4-Hydroxylase Subunit Alpha-2
Chain: A
Synonym: 4-Ph Alpha-2,Procollagen-Proline,2-Oxoglutarate-4- Dioxygenase Subunit Alpha-2;
Ec: 1.14.11.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: P4ha2, Unq290pro330
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)Plyss
Expression_system_vector_type: Pett22b(+)

Molecule: Pro-9
Chain: C
Engineered: Yes
Other_details: Synthetic Peptide Having 9 Proline Residues.

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 32 2 1
R_factor 0.170 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.899 56.899 67.871 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand DMS, SO4 enzyme Oxidoreductase E.C.1.14.11.2 BRENDA
Primary referenceStructural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): high affinity peptides have a PxGP sequence motif., Murthy AV, Sulu R, Koski MK, Tu H, Anantharajan J, Sah-Teli SK, Myllyharju J, Wierenga RK, Protein Sci. 2018 Aug 30. doi: 10.1002/pro.3450. PMID:30168208
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (6evm.pdb1.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 6EVM
  • CSU: Contacts of Structural Units for 6EVM
  • Structure Factors (124 Kb)
  • Retrieve 6EVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EVM from S2C, [Save to disk]
  • View 6EVM 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.
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  • Visual 3D analysis of 6EVM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6evm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6evm_A] [6evm_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6EVM
  • Community annotation for 6EVM at PDBWiki (http://pdbwiki.org)

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