2D3H - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY) 4-HYP-HYP-GLY-(PRO-PRO-GLY)4

Authors :   G. Wu, K. Noguchi, K. Okuyama, K. Mizuno, H. P. Bachinger

Date :   28 Sep 05 (Deposition) - 19 Sep 06 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.22

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Collagen, Crystal Structure, Triple-Helix, Hydroxyproline, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Okuyama, C. Hongo, G. Wu, K. Mizuno, K. Noguchi, S. Ebisuzaki, Y. Tanaka, N. Nishino, H. P. Bachinger
High-Resolution Structures Of Collagen-Like Peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro- Gly)(4)]: Implications For Triple-Helix Hydration And Hyp(X) Puckering.
Biopolymers V. 91 361 2009
PubMed-ID: 19137577 | Reference-DOI: 10.1002/BIP.21138
(for further references see the PDB file header)

Molecule 1 - COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP- GLY-(PRO-PRO-GLY)4
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Other Details	:	THIS COLLAGEN MODEL TRIPLETT WAS CHEMICALLY SYSTHESIZED. HYP-HYP-GLY GUEST IN PRO-PRO-GLY HOST PEPTIDE.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	HYP	12	Mod. Amino Acid	4-HYDROXYPROLINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	HYP	6	Mod. Amino Acid	4-HYDROXYPROLINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	HYP	6	Mod. Amino Acid	4-HYDROXYPROLINE

(no "Site" information available for 2D3H)

(no "SS Bond" information available for 2D3H)

(no "Cis Peptide Bond" information available for 2D3H)

(no "SAP(SNP)/Variant" information available for 2D3H)

(no "PROSITE Motif" information available for 2D3H)

(no "Exon" information available for 2D3H)

Asymmetric Unit

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:24
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:24
                                    52        62    
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                  2d3h A  1 PPGPPGPPGPPGppGPPGPPGPPG 24
                                    10  ||    20    
                                       13-HYP       
                                        14-HYP

Chain B from PDB  Type:PROTEIN  Length:24
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:24
                                    52        62    
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                  2d3h B  1 PPGPPGPPGPPGppGPPGPPGPPG 24
                                    10  ||    20    
                                       13-HYP       
                                        14-HYP

Chain C from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    49        59     
           Q80BK4_SHV2   40 PPGPPGPPGPPGPPGPPGPPGPPGP 64
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2d3h C  1 PPGPPGPPGPPGppGPPGPPGPPGP 25
                                    10  ||    20     
                                       13-HYP        
                                        14-HYP

Chain D from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    51        61     
           Q80BK4_SHV2   42 GPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2d3h D  3 GPPGPPGPPGppGPPGPPGPPGPPG 27
                                    12||      22     
                                     13-HYP          
                                      14-HYP

Chain E from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    50        60     
           Q80BK4_SHV2   41 PGPPGPPGPPGPPGPPGPPGPPGPP 65
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2d3h E  2 PGPPGPPGPPGppGPPGPPGPPGPP 26
                                    11 ||     21     
                                      13-HYP         
                                       14-HYP

Chain F from PDB  Type:PROTEIN  Length:24
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:24
                                    52        62    
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                  2d3h F  4 PPGPPGPPGppGPPGPPGPPGPPG 27
                                    13|       23    
                                    13-HYP          
                                     14-HYP

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 '\|'

(no "SCOP Domain" information available for 2D3H)

(no "CATH Domain" information available for 2D3H)

(no "Pfam Domain" information available for 2D3H)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q80BK4_SHV2 | Q80BK4)

cellular component
	GO:0016021		integral component of membrane		The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020		membrane		A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Sites
(no "Sites" information available for 2d3h)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d3h)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2d3h
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UniProtKB/TrEMBL
	Q80BK4_SHV2 \| Q80BK4	:	1k6f 1wzb 1x1k 1ym8 2cuo 2d3f 3ah9 3ai6 3b0s 3b2c

1v4f	CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- GLY SEQUENCE AT 1.3A
1v6q	CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- GLY SEQUENCE AT 1.3A
1v7h	CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- GLY SEQUENCE AT 1.26A
1x1k	HOST-GUEST PEPTIDE (PRO-PRO-GLY)4-(PRO-ALLOHYP-GLY)-(PRO- PRO-GLY)4
1ym8	CRYSTAL STRUCTURE OF GZZ SHOWS UP PUCKERING OF THE PROLINE RING IN THE XAA POSITION
2cuo	COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
2d3f	CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY) 4-PRO-HYP-GLY-(PRO-PRO-GLY)4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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