2D5X - JenaLib

Title :   CRYSTAL STRUCTURE OF CARBONMONOXY HORSE HEMOGLOBIN COMPLEXED WITH L35

Authors :   T. Yokoyama, S. Neya, A. Tsuneshige, T. Yonetani, S. Y. Park, J. R. Tame

Date :   08 Nov 05 (Deposition) - 07 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Hemoglobin, L35, Allosteric Effector, Crystal Structure, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yokoyama, S. Neya, A. Tsuneshige, T. Yonetani, S. Y. Park, J. R. Tame
R-State Haemoglobin With Low Oxygen Affinity: Crystal Structures Of Deoxy Human And Carbonmonoxy Horse Haemoglobin Bound To The Effector Molecule L35
J. Mol. Biol. V. 356 790 2006
PubMed-ID: 16403522 | Reference-DOI: 10.1016/J.JMB.2005.12.018
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:58 , LYS A:61 , LEU A:83 , LEU A:86 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , LEU A:136 , CMO A:1143 , L35 A:1200 , HOH A:1248 , HOH A:1258 , HOH A:1263	BINDING SITE FOR RESIDUE HEM A 142
2	AC2	SOFTWARE	LEU A:29 , HIS A:58 , VAL A:62 , HEM A:142	BINDING SITE FOR RESIDUE CMO A 1143
3	AC3	SOFTWARE	THR B:38 , PHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , SER B:70 , PHE B:71 , LEU B:88 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , CMO B:1148 , HOH B:1228 , HOH B:1254	BINDING SITE FOR RESIDUE HEM B 147
4	AC4	SOFTWARE	HIS B:63 , VAL B:67 , HEM B:147	BINDING SITE FOR RESIDUE CMO B 1148
5	AC5	SOFTWARE	LEU A:68 , ASN A:82 , LEU A:83 , ASP A:85 , LEU A:86 , LYS A:90 , HEM A:142 , HOH A:1263 , HOH A:1305	BINDING SITE FOR RESIDUE L35 A 1200
6	AC6	SOFTWARE	LYS A:99 , LEU A:100 , HIS A:103 , SER A:130 , THR A:137 , HOH A:1229 , HOH A:1243 , TYR B:35 , TRP B:37 , LEU B:105 , ASN B:108 , HOH B:1234 , HOH B:1287 , HOH B:1301	BINDING SITE FOR RESIDUE L35 B 1201

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:141
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 142
               SCOP domains d2d5xa_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 2d5xA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q--------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5x A   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_HORSE | P02062 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_HORSE     1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
               SCOP domains d2d5xb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 2d5xB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --GLOBIN  PDB: B:3-146 UniProt: 3-146                                                                                                              PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5x B   1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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 (2, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 16)

Asymmetric Unit(hide GO term definitions)

Chain A (HBA_HORSE | P01958)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.
cellular component
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B (HBB_HORSE | P02062)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.
cellular component
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

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