OCA Atlas for 3MK1

3MK1

Hydrolase

date

Apr 13, 2010

title

Refinement Of Placental Alkaline Phosphatase Complexed With Nitrophenyl

authors

B.Stec, A.Cheltsov, J.L.Millan

compound

source

Molecule: Alkaline Phosphatase, Placental Type
Chain: A
Synonym: Placental Alkaline Phosphatase 1, Plap-1, Alkaline Phosphatase Regan Isozyme;
Ec: 3.1.3.1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

symmetry

Space Group: C 2 2 21

R_factor

0.139

R_Free

0.178

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
88.346	114.573	106.568	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.57 Å

ligand

ACT, CA, MG, NA, NAG, NPO, PO4, SEP, ZN

enzyme

Hydrolase E.C.3.1.3.1 BRENDA

note

3MK1 is a representative structure

Gene
Ontology

Chain	Function	Process	Component
A

Primary reference

Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site., Stec B, Cheltsov A, Millan JL, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Aug 1;66(Pt, 8):866-70. Epub 2010 Jul 27. PMID:20693656

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]

Biological Unit Coordinates (3mk1.pdb1.gz) 350 Kb

LPC: Ligand-Protein Contacts for 3MK1

CSU: Contacts of Structural Units for 3MK1

Structure Factors (1130 Kb)

Retrieve 3MK1 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3MK1 from S2C, [Save to disk]

Re-refined 3mk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3MK1 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 3MK1

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3MK1, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3mk1_A] [3mk1]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domain found in 3MK1: [alkPPc ] by SMART

Other resources with information on 3MK1

Community annotation for 3MK1 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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