3GLN - JenaLib

Title :   CARBONMONOXY NGB UNDER XENON PRESSURE

Authors :   T. Moschetti, U. Mueller, J. Schultze, M. Brunori, B. Vallone

Date :   12 Mar 09 (Deposition) - 22 Sep 09 (Release) - 22 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.26

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

Keywords :   Neuroglobin, Hemeprotein, Xenon Binding, Cavities, Oxygen Storage/Transport Protein Complex, Heme, Iron, Metal- Binding, Oxygen Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Moschetti, U. Mueller, J. Schultze, M. Brunori, B. Vallone
The Structure Of Neuroglobin At High Xe And Kr Pressure Reveals Partial Conservation Of Globin Internal Cavities
Biophys. J. V. 97 1700 2009
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CMO	1	Ligand/Ion	CARBON MONOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	1	Ligand/Ion	SULFATE ION
4	XE	4	Ligand/Ion	XENON

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CMO	1	Ligand/Ion	CARBON MONOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	1	Ligand/Ion	SULFATE ION
4	XE	-1	Ligand/Ion	XENON

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CMO	2	Ligand/Ion	CARBON MONOXIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION
4	XE	-1	Ligand/Ion	XENON

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:19 , PRO A:20 , LEU A:21 , GLU A:22 , ARG A:66	BINDING SITE FOR RESIDUE SO4 A 152
2	AC2	SOFTWARE	TYR A:88 , HEM A:158	BINDING SITE FOR RESIDUE XE A 153
3	AC3	SOFTWARE	ALA A:29 , PHE A:32 , SER A:55 , LEU A:56	BINDING SITE FOR RESIDUE XE A 154
4	AC4	SOFTWARE	TRP A:133 , LEU A:136	BINDING SITE FOR RESIDUE XE A 155
5	AC5	SOFTWARE	HEM A:158	BINDING SITE FOR RESIDUE XE A 156
6	AC6	SOFTWARE	PHE A:28 , HIS A:64 , HIS A:96 , HEM A:158	BINDING SITE FOR RESIDUE CMO A 157
7	AC7	SOFTWARE	LEU A:41 , PHE A:42 , TYR A:44 , HIS A:64 , LYS A:67 , VAL A:68 , VAL A:71 , TYR A:88 , LEU A:92 , LYS A:95 , HIS A:96 , VAL A:101 , SER A:105 , PHE A:106 , VAL A:109 , TYR A:137 , VAL A:140 , MET A:144 , XE A:153 , XE A:156 , CMO A:157 , HOH A:165 , HOH A:172 , HOH A:184	BINDING SITE FOR RESIDUE HEM A 158

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

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
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Chain A from PDB  Type:PROTEIN  Length:146
 aligned with NGB_MOUSE | Q9ER97 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:146
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142      
            NGB_MOUSE     3 RPESELIRQSWRVVSRSPLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLTSLGRKHRAVGVRLSSFSTVGESLLYMLEKCLGPDFTPATRTAWSRLYGAVVQAMSRGW 148
               SCOP domains d3glna_ A: Neuroglobin                                                                                                                             SCOP domains
               CATH domains 3glnA00 A:3-148 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: A:5-144 UniProt: 5-144                                                                                                         ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gln A   3 RPESELIRQSWRVVSRSPLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDSLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLTSLGRKHRAVGVRLSSFSTVGESLLYMLEKSLGPDFTPATRTAWSRLYGAVVQAMSRGW 148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

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	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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (NGB_MOUSE | Q9ER97)

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.
	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).
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0043204	perikaryon	The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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