OCA Atlas for 1NDM

1NDM

Immune System Hydrolase

date

Dec 09, 2002

title

Crystal Structure Of Fab Fragment Of Antibody Hyhel-26 Complexed With Lysozyme

authors

R.A.Mariuzza, Y.Li, H.Li

compound

source

Molecule: Antibody Kappa Light Chain
Chain: A
Fragment: Light Chain
Engineered: Yes
Other_details: First Chain Of Anti-Lysozyme Antibody Hyhel- 26;

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Immunoglobulin Gamma 1 Chain
Chain: B
Engineered: Yes
Other_details: Second Chain Of Anti-Lysozyme Antibody Hyhel-26;

Molecule: Lysozyme C
Chain: C
Synonym: 1,4-Beta-N-Acetylmuramidase C; Allergen Gal D 4 Gal D Iv;
Ec: 3.2.1.17
Engineered: Yes
Mutation: Yes

Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9

symmetry

Space Group: P 21 21 2

R_factor

0.208

R_Free

0.258

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
90.680	164.020	40.000	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.10 Å

ligand

enzyme

Hydrolase E.C.3.2.1.17 BRENDA

related structures

by homologous chain: 1NC2, 1SY6, 1XEJ, 1YEK, 2LZ2

Gene
Ontology

Chain	Function	Process	Component
A
C

Primary reference

X-ray snapshots of the maturation of an antibody response to a protein antigen., Li Y, Li H, Yang F, Smith-Gill SJ, Mariuzza RA, Nat Struct Biol 2003 Jun;10(6):482-8. PMID:12740607

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]

Biological Unit Coordinates (1ndm.pdb1.gz) 100 Kb

CSU: Contacts of Structural Units for 1NDM

Likely Quarternary Molecular Structure file(s) for 1NDM

Structure Factors (241 Kb)

Retrieve 1NDM in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1NDM from S2C, [Save to disk]

Re-refined 1ndm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1NDM 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 1NDM

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 1NDM, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ndma1, region A:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1ndma2, region A:108-214 [Jmol] [rasmolscript] [script source]
- Domain d1ndmb1, region B:301-413 [Jmol] [rasmolscript] [script source]
- Domain d1ndmb2, region B:414-521 [Jmol] [rasmolscript] [script source]
- Domain d1ndmc_, region C [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ndm_B] [1ndm_A] [1ndm] [1ndm_C]

SWISS-PROT database: [P01865] [P01837] [P00698]

Domain organization of [GCAM_MOUSE] [IGKC_MOUSE] [LYSC_CHICK] by SWISSPFAM

Domains found in 1NDM: [IG_like] [IGv] [LYZ1 ] by SMART

Other resources with information on 1NDM

Community annotation for 1NDM 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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