1YCB - JenaLib

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Title :   DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND CARBONMONOXY FORMS OF A THREONINE68 (E11) MUTANT INVESTIGATED BY X-RAY CRYSTALLOGRAPHY AND INFRARED SPECTROSCOPY

Authors :   A. D. Cameron, S. J. Smerdon, A. J. Wilkinson, J. Habash, J. R. Helliwell

Date :   10 Aug 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxygen Storage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. D. Cameron, S. J. Smerdon, A. J. Wilkinson, J. Habash, J. R. Helliwell, T. Li, J. S. Olson
Distal Pocket Polarity In Ligand Binding To Myoglobin: Deoxy And Carbonmonoxy Forms Of A Threonine68(E11) Mutant Investigated By X-Ray Crystallography And Infrared Spectroscopy.
Biochemistry V. 32 13061 1993
PubMed-ID: 8241160 | Reference-DOI: 10.1021/BI00211A016
(for further references see the PDB file header)

Molecule 1 - MYOGLOBIN
	Chains	:	A, B
	Engineered	:	YES
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:42 , PHE A:43 , HIS A:64 , THR A:68 , LEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , PHE A:138 , HOH A:160 , HOH A:196 , HOH A:197	BINDING SITE FOR RESIDUE HEM A 154
2	AC2	SOFTWARE	LYS B:42 , PHE B:43 , HIS B:64 , THR B:68 , ALA B:71 , LEU B:89 , SER B:92 , HIS B:93 , HIS B:97 , ILE B:99 , TYR B:103 , PHE B:138 , HOH B:191	BINDING SITE FOR RESIDUE HEM B 154

(no "SS Bond" information available for 1YCB)

(no "Cis Peptide Bond" information available for 1YCB)

(no "SAP(SNP)/Variant" information available for 1YCB)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	MYG_PIG	3-148	2	A:2-147 B:2-147

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	MYG_PIG	3-148	1	A:2-147 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	MYG_PIG	3-148	1	- B:2-147

(no "Exon" information available for 1YCB)

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
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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with MYG_PIG | P02189 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
              MYG_PIG     2 GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGNTVLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG 154
               SCOP domains d1ycba_ A: Myoglobin                                                                                                                                      SCOP domains
               CATH domains 1ycbA00 A:1-153 Globins                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ycb A   1 GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGNTTLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with MYG_PIG | P02189 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
              MYG_PIG     2 GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGNTVLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG 154
               SCOP domains d1ycbb_ B: Myoglobin                                                                                                                                      SCOP domains
               CATH domains 1ycbB00 B:1-153 Globins                                                                                                                                   CATH domains
           Pfam domains (1) -----Globin-1ycbB01 B:6-112                                                                                     ----------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-1ycbB02 B:6-112                                                                                     ----------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ycb B   1 GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGNTTLTALGGILKKKGHHEAELTPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Myoglobin (324)

Pig (Sus scrofa) [TaxId: 9823] (17)

1a	d1ycba_	A:
1b	d1ycbb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Pig (Sus scrofa) (19)

1a	1ycbA00	A:1-153
1b	1ycbB00	B:1-153

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Sus scrofa (Pig) (19)

1a	Globin-1ycbB01	B:6-112
1b	Globin-1ycbB02	B:6-112

Asymmetric Unit(hide GO term definitions)

Chain A,B (MYG_PIG | P02189)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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