1M3D	Structural Protein	date	Jun 27, 2002
title	Structure Of Type Iv Collagen Nc1 Domains
authors	M.Sundaramoorthy, M.Meiyappan, P.Todd, B.G.Hudson
compound		source
Molecule: Type Iv Collagen Noncollagenous Domain- Alpha1 Chain: A, B, D, E, G, H, J, K Fragment: Nc1 Domain (Residues 1-229)		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Other_details: Bovine Eye Lens Capsule
Molecule: Type Iv Collagen Noncollagenous Domain- Alpha2 Chain: C, F, I, L Fragment: Nc1 Domain (Residues 1-227)		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Other_details: Bovine Eye Lens Capsule
symmetry	Space Group: P 1 21 1	R_factor 0.169 R_Free 0.197
crystal cell	length a length b length c angle alpha angle beta angle gamma 80.069 137.963 127.131 90.00 90.31 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	BR, GOL, LU	enzyme
related structures	by homologous chain: 1LI1
Gene Ontology	Chain Function Process Component A, J, K, E, B, H, D, G F, C, I, L
Primary reference	Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes., Sundaramoorthy M, Meiyappan M, Todd P, Hudson BG, J Biol Chem 2002 Aug 23;277(34):31142-53. Epub 2002 Apr 22. PMID:11970952

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (451 Kb) [Save to disk] Biological Unit Coordinates (1m3d.pdb1.gz) 228 Kb Biological Unit Coordinates (1m3d.pdb2.gz) 225 Kb LPC: Ligand-Protein Contacts for 1M3D CSU: Contacts of Structural Units for 1M3D Likely Quarternary Molecular Structure file(s) for 1M3D Structure Factors (1396 Kb) Retrieve 1M3D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1M3D from S2C, [Save to disk] Re-refined 1m3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1M3D 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 1M3D

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 1M3D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m3da2, region A:115-227 [Jmol] [rasmolscript] [script source]     - Domain d1m3da1, region A:5-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3db2, region B:115-229 [Jmol] [rasmolscript] [script source]     - Domain d1m3db1, region B:6-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dc2, region C:115-226 [Jmol] [rasmolscript] [script source]     - Domain d1m3dc1, region C:5-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dd2, region D:115-228 [Jmol] [rasmolscript] [script source]     - Domain d1m3dd1, region D:4-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3de2, region E:115-227 [Jmol] [rasmolscript] [script source]     - Domain d1m3de1, region E:4-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3df2, region F:115-226 [Jmol] [rasmolscript] [script source]     - Domain d1m3df1, region F:4-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dg2, region G:115-228 [Jmol] [rasmolscript] [script source]     - Domain d1m3dg1, region G:4-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dh2, region H:115-227 [Jmol] [rasmolscript] [script source]     - Domain d1m3dh1, region H:4-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3di2, region I:115-226 [Jmol] [rasmolscript] [script source]     - Domain d1m3di1, region I:5-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dj2, region J:115-227 [Jmol] [rasmolscript] [script source]     - Domain d1m3dj1, region J:5-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dk2, region K:115-229 [Jmol] [rasmolscript] [script source]     - Domain d1m3dk1, region K:6-114 [Jmol] [rasmolscript] [script source]     - Domain d1m3dl2, region L:115-226 [Jmol] [rasmolscript] [script source]     - Domain d1m3dl1, region L:5-114 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1m3d_F] [1m3d_I] [1m3d_J] [1m3d_G] [1m3d_B] [1m3d_L] [1m3d_E] [1m3d] [1m3d_H] [1m3d_K] [1m3d_A] [1m3d_C] [1m3d_D] SWISS-PROT database: [Q7SIB2] [Q7SIB3] Domain organization of [CO4A1_BOVIN] [CO4A2_BOVIN] by SWISSPFAM Domain found in 1M3D: [C4 ] by SMART

Other resources with information on 1M3D

Community annotation for 1M3D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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