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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN METHAEMOGLOBIN COMPLEXED WITH THE SECOND NEAT DOMAIN OF ISDH FROM STAPHYLOCOCCUS AUREUS
 
Authors :  K. Krishna Kumar, D. A. Jacques, J. M. Guss, D. A. Gell
Date :  24 May 12  (Deposition) - 29 May 13  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B,E
Biol. Unit 1:  A (1x),B (1x),E (1x)
Keywords :  Globin Fold, Ig Fold, Oxygen Transport, Haem Acquisition, Oxygen Binding, Haem Binding, Cell Wall, Oxygen Transport-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. F. Dickson, K. Krishna Kumar, D. A. Jacques, G. R. Malmirchegini, T. Spirig, J. P. Mackay, R. T. Clubb, J. M. Guss, D. A. Gell
Structure Of The Hemoglobin-Isdh Complex Reveals The Molecular Basis Of Iron Capture By Staphylococcus Aureus
J. Biol. Chem. V. 289 6728 2014
PubMed-ID: 24425866  |  Reference-DOI: 10.1074/JBC.M113.545566

(-) Compounds

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-GLOBIN, HEMOGLOBIN ALPHA CHAIN
 
Molecule 2 - HEMOGLOBIN SUBUNIT BETA
    Chains: B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-GLOBIN, HEMOGLOBIN BETA CHAIN, LVV-HEMORPHIN-7
 
Molecule 3 - IRON-REGULATED SURFACE DETERMINANT PROTEIN H
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SECOND NEAT DOMAIN
    Gene: ISDH
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 196620
    Strain: MW2
    Synonym: HAPTOGLOBIN RECEPTOR A, STAPHYLOCOCCUS AUREUS SURFACE PROTEIN I

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABE
Biological Unit 1 (1x): A (1x)B (1x)E (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HEM-1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , PHE A:43 , HIS A:45 , PHE A:46 , 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 , HOH A:308 , ASP E:39BINDING SITE FOR RESIDUE HEM A 201
2AC2SOFTWARETHR B:38 , PHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , PHE B:71 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , LEU B:106 , VAL B:137 , LEU B:141 , HOH B:308 , LYS E:61 , ARG E:113BINDING SITE FOR RESIDUE HEM B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FC3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu E:53 -Pro E:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FC3)

(-) Exons   (0, 0)

(no "Exon" information available for 4FC3)

(-) 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:140
                                                                                                                                                                            
               SCOP domains d4fc3a_ A: Hemoglobin, alpha-chain                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fc3 A   1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains d4fc3b_ B: Hemoglobin, beta-chain                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fc3 B   1 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAH 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain E from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains d4fc3e_ E: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh..............eeee.eeee......hhhhhhh....eeeeee..eeeeeeee.....eeeeeeee..ee...eeeeee....eeeeeee......eeeeeeeeee...eeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fc3 E   1 QQYPPADESLQDAIKNPAIIDKEHTADNWRPIDFQMKNDKGERQFYHYASTVEPATVIFTKTGPIIELGLKTASTWKKFEVYEGDKKLPVELVSYDSDKDYAYIRFPVSNGTREVKIVSSIEYGENIHEDYDYTLMVFAQPITN 144
                                    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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FC3)

(-) Gene Ontology  (35, 61)

Asymmetric Unit(hide GO term definitions)

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  4fc3
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  HBA_HUMAN | P69905
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  HBB_HUMAN | P68871
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  ISDH_STAAW | Q8NW39
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HBA_HUMAN | P69905: 1a00 1a01 1a0u 1a0z 1a3n 1a3o 1a9w 1abw 1aby 1aj9 1b86 1bab 1bbb 1bij 1buw 1bz0 1bz1 1bzz 1c7b 1c7c 1c7d 1cls 1cmy 1coh 1dke 1dxt 1dxu 1dxv 1fdh 1fn3 1g9v 1gbu 1gbv 1gli 1gzx 1hab 1hac 1hba 1hbb 1hbs 1hco 1hdb 1hga 1hgb 1hgc 1hho 1ird 1j3y 1j3z 1j40 1j41 1j7s 1j7w 1j7y 1jy7 1k0y 1k1k 1kd2 1lfl 1lfq 1lft 1lfv 1lfy 1lfz 1ljw 1m9p 1mko 1nej 1nih 1nqp 1o1i 1o1j 1o1k 1o1l 1o1m 1o1n 1o1o 1o1p 1qi8 1qsh 1qsi 1qxd 1qxe 1r1x 1r1y 1rps 1rq3 1rq4 1rqa 1rvw 1sdk 1sdl 1shr 1si4 1thb 1uiw 1vwt 1xxt 1xy0 1xye 1xz2 1xz4 1xz5 1xz7 1xzu 1xzv 1y01 1y09 1y0a 1y0c 1y0d 1y0t 1y0w 1y22 1y2z 1y31 1y35 1y45 1y46 1y4b 1y4f 1y4g 1y4p 1y4q 1y4r 1y4v 1y5f 1y5j 1y5k 1y7c 1y7d 1y7g 1y7z 1y83 1y85 1y8w 1ydz 1ye0 1ye1 1ye2 1yen 1yeo 1yeq 1yeu 1yev 1yff 1yg5 1ygd 1ygf 1yh9 1yhe 1yhr 1yie 1yih 1yvq 1yvt 1yzi 1z8u 2d5z 2d60 2dn1 2dn2 2dn3 2dxm 2h35 2hbc 2hbd 2hbe 2hbf 2hbs 2hco 2hhb 2hhd 2hhe 2m6z 2w6v 2w72 2yrs 3b75 3d17 3d7o 3dut 3hhb 3hxn 3ia3 3ic0 3ic2 3kmf 3nl7 3nmm 3odq 3onz 3oo4 3oo5 3ovu 3p5q 3qjb 3qjc 3qjd 3qje 3r5i 3s48 3s65 3s66 3szk 3wcp 3whm 4hhb 4ij2 4l7y 4m4a 4m4b 4mqc 4mqg 4mqh 4mqi 4mqj 4mqk 4n7n 4n7o 4n7p 4n8t 4ni0 4ni1 4rol 4rom 4wjg 4x0l 4xs0 5e29 5e6e 5e83 5ee4 5hu6 5hy8 5jdo 5kdq 5me2 5ni1 5sw7 5u3i 5ucu 5ufj 5urc 6hbw
        HBB_HUMAN | P68871: 1a00 1a01 1a0u 1a0z 1a3n 1a3o 1abw 1aby 1aj9 1b86 1bab 1bbb 1bij 1buw 1bz0 1bz1 1bzz 1c7b 1c7c 1c7d 1cbl 1cbm 1ch4 1cls 1cmy 1coh 1dke 1dxt 1dxu 1dxv 1fn3 1g9v 1gbu 1gbv 1gli 1gzx 1hab 1hac 1hba 1hbb 1hbs 1hco 1hdb 1hga 1hgb 1hgc 1hho 1ird 1j3y 1j3z 1j40 1j41 1j7s 1j7w 1j7y 1jy7 1k0y 1k1k 1kd2 1lfl 1lfq 1lft 1lfv 1lfy 1lfz 1ljw 1m9p 1mko 1nej 1nih 1nqp 1o1i 1o1j 1o1k 1o1l 1o1m 1o1n 1o1o 1o1p 1qi8 1qsh 1qsi 1qxd 1qxe 1r1x 1r1y 1rps 1rq3 1rq4 1rqa 1rvw 1sdk 1sdl 1thb 1uiw 1vwt 1xxt 1xy0 1xye 1xz2 1xz4 1xz5 1xz7 1xzu 1xzv 1y09 1y0a 1y0c 1y0d 1y0t 1y0w 1y22 1y2z 1y31 1y35 1y45 1y46 1y4b 1y4f 1y4g 1y4p 1y4q 1y4r 1y4v 1y5f 1y5j 1y5k 1y7c 1y7d 1y7g 1y7z 1y83 1y85 1y8w 1ydz 1ye0 1ye1 1ye2 1yen 1yeo 1yeq 1yeu 1yev 1yff 1yg5 1ygd 1ygf 1yh9 1yhe 1yhr 1yie 1yih 1yvq 1yvt 1yzi 2d5z 2d60 2dn1 2dn2 2dn3 2dxm 2h35 2hbc 2hbd 2hbe 2hbf 2hbs 2hco 2hhb 2hhd 2hhe 2m6z 2w6v 2w72 2yrs 3b75 3d17 3d7o 3dut 3hhb 3hxn 3ic0 3ic2 3kmf 3nl7 3nmm 3odq 3onz 3oo4 3oo5 3p5q 3qjb 3qjc 3qjd 3qje 3r5i 3s65 3s66 3szk 3w4u 3wcp 3whm 4hhb 4ij2 4l7y 4m4a 4m4b 4mqc 4mqg 4mqh 4mqi 4n7n 4n7o 4n7p 4n8t 4ni0 4ni1 4rol 4rom 4wjg 4x0l 4xs0 5e29 5e6e 5e83 5ee4 5hu6 5hy8 5jdo 5kdq 5me2 5ni1 5sw7 5u3i 5ucu 5ufj 5urc 6hbw
        ISDH_STAAW | Q8NW39: 2lhr 3szk

(-) Related Entries Specified in the PDB File

3ovu 3s48 3szk