1LD0 - JenaLib

Title :   THEORETICAL MODEL OF HUMAN GAMMA D CRYSTALLIN

Authors :   A. Salim, Z. H. Zaidi

Date :   08 Apr 02 (Deposition) - 24 Apr 02 (Release) - 07 Jan 03 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Gamma Crystallin, Theoretical Model, Eye Lens Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Salim, Z. H. Zaidi
Homology Models Of Human Gamma-Crystallins: Structural Study Of The Extensive Charge Network In Gamma-Crystallins
Biochem. Biophys. Res. Comm. V. 300 624 2003
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

Theoretical Model (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010733	R	15	C	CRGD_HUMAN	Disease (CTRCT4)	121909595	A	R	14	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	P	23	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	P	23	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	A	R	36	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	A	W	42	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	A	R	58	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	A	M	101	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	A	E	106	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 4)

Exons (3, 3)

Sequences/Alignments

Theoretical Model

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:173
 aligned with CRGD_HUMAN | P07320 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:173
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   
           CRGD_HUMAN     2 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 174
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeeee......hhhhh....eeeeee.eeeee.hhhhh..eeee..eee.hhhhhh.......eeeee......eeeeeeehhheeeeeee.....hhhhhh......eeeeee..eeeeee...eeeeeee..eee.hhhhhh.......eeee..... Sec.struct. author
             SAPs(SNPs) (1) -------------C--------S------------S-----R---------------H------------------------------------------V----A------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------T------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE CRYSTALLIN_BETA_GAMMA  PDB: A:1-39     CRYSTALLIN_BETA_GAMMA  PDB: A:40-82        ----CRYSTALLIN_BETA_GAMMA  PDB: A:87-127     CRYSTALLIN_BETA_GAMMA  PDB: A:128-170      --- PROSITE
               Transcript 1 1.Exon 1.2  PDB: A:3-83 UniProt: 4-84                                              Exon 1.3  PDB: A:84-173 UniProt: 85-174                                                    Transcript 1
                 1ld0 A   1 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Theoretical Model(hide GO term definitions)

Chain A (CRGD_HUMAN | P07320)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005212	structural constituent of eye lens	The action of a molecule that contributes to the structural integrity of the lens of an eye.
biological process
	GO:0034614	cellular response to reactive oxygen species	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
	GO:0002088	lens development in camera-type eye	The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
	GO:0070306	lens fiber cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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