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(-) Description

Title :  INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C)
 
Authors :  N. Gerber, H. Lowman, D. R. Artis, C. Eigenbrot
Date :  13 Jul 99  (Deposition) - 22 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Intercrine Alpha Family, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Gerber, H. Lowman, D. R. Artis, C. Eigenbrot
Receptor-Binding Conformation Of The "Elr" Motif Of Il-8: X-Ray Structure Of The L5C/H33C Variant At 2. 35 A Resolution.
Proteins V. 38 361 2000 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERLEUKIN-8 VARIANT
    CellMONOCYTE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO C:16 , PHE C:17 , HOH C:136 , SER D:1 , ARG D:6 , HOH D:224BINDING SITE FOR RESIDUE SO4 D 101
2AC2SOFTWAREALA B:2 , LYS B:3 , GLU B:4 , CYS B:5 , ASN B:56 , ARG B:60 , HOH B:169BINDING SITE FOR RESIDUE SO4 B 134
3AC3SOFTWAREHIS D:18 , PRO D:19 , LYS D:20 , HOH D:282BINDING SITE FOR RESIDUE SO4 D 190

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:5 -A:33
2A:7 -A:34
3A:9 -A:50
4B:5 -B:33
5B:7 -B:34
6B:9 -B:50
7C:7 -C:34
8C:9 -C:50
9D:5 -D:33
10D:7 -D:34
11D:9 -D:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QE6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QE6)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.IL8_HUMAN34-79
 
 
 
  4A:7-52
B:7-52
C:7-52
D:7-52
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.IL8_HUMAN34-79
 
 
 
  2A:7-52
B:7-52
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.IL8_HUMAN34-79
 
 
 
  2-
-
C:7-52
D:7-52
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.IL8_HUMAN34-79
 
 
 
  4A:7-52
B:7-52
C:7-52
D:7-52

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003074071aENSE00001816394chr4:74606223-74606439217IL8_HUMAN1-22220--
1.2aENST000003074072aENSE00001141340chr4:74607259-74607394136IL8_HUMAN22-67464A:5-40
B:2-40
C:6-40
D:1-40
36
39
35
40
1.2cENST000003074072cENSE00001127428chr4:74607666-7460774984IL8_HUMAN67-95294A:40-68
B:40-68
C:40-68
D:40-68
29
29
29
29
1.3ENST000003074073ENSE00001211447chr4:74608166-746094331268IL8_HUMAN95-9954A:68-72
B:68-72
C:68-72
D:68-72
5
5
5
5

(-) 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:68
 aligned with IL8_HUMAN | P10145 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:68
                                    41        51        61        71        81        91        
             IL8_HUMAN   32 LRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 99
               SCOP domains d1qe6a_ A: Interleukin-8, IL-8                                       SCOP domains
               CATH domains 1qe6A00 A:5-72  [code=2.40.50.40, no name defined]                   CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SMALL_CYTOKINES_CXC  PDB: A:7-52              -------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:5-40 [INCOMPLETE] ---------------------------1.3   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.2c  PDB: A:40-68      ---- Transcript 1 (2)
                  1qe6 A  5 CRCQCIKTYSKPFHPKFIKELRVIESGPCCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 72
                                    14        24        34        44        54        64        

Chain B from PDB  Type:PROTEIN  Length:71
 aligned with IL8_HUMAN | P10145 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:71
                                    38        48        58        68        78        88        98 
             IL8_HUMAN   29 AKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 99
               SCOP domains d1qe6b_ B: Interleukin-8, IL-8                                          SCOP domains
               CATH domains 1qe6B00 B:2-72  [code=2.40.50.40, no name defined]                      CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SMALL_CYTOKINES_CXC  PDB: B:7-52              -------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:2-40 UniProt: 22-67  ---------------------------1.3   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.2c  PDB: B:40-68      ---- Transcript 1 (2)
                  1qe6 B  2 AKECRCQCIKTYSKPFHPKFIKELRVIESGPCCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 72
                                    11        21        31        41        51        61        71 

Chain C from PDB  Type:PROTEIN  Length:67
 aligned with IL8_HUMAN | P10145 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:67
                                    42        52        62        72        82        92       
             IL8_HUMAN   33 RCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 99
               SCOP domains d1qe6c_ C: Interleukin-8, IL-8                                      SCOP domains
               CATH domains 1qe6C00 C:6-72  [code=2.40.50.40, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SMALL_CYTOKINES_CXC  PDB: C:7-52              -------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:6-40 [INCOMPLETE]---------------------------1.3   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.2c  PDB: C:40-68      ---- Transcript 1 (2)
                  1qe6 C  6 RCQCIKTYSKPFHPKFIKELRVIESGPCCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 72
                                    15        25        35        45        55        65       

Chain D from PDB  Type:PROTEIN  Length:72
 aligned with IL8_HUMAN | P10145 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:72
                                    37        47        57        67        77        87        97  
             IL8_HUMAN   28 SAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 99
               SCOP domains d1qe6d_ D: Interleukin-8, IL-8                                           SCOP domains
               CATH domains 1qe6D00 D:1-72  [code=2.40.50.40, no name defined]                       CATH domains
           Pfam domains (1) IL8-1qe6D01 D:1-66                                                ------ Pfam domains (1)
           Pfam domains (2) IL8-1qe6D02 D:1-66                                                ------ Pfam domains (2)
           Pfam domains (3) IL8-1qe6D03 D:1-66                                                ------ Pfam domains (3)
           Pfam domains (4) IL8-1qe6D04 D:1-66                                                ------ Pfam domains (4)
         Sec.struct. author .................hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SMALL_CYTOKINES_CXC  PDB: D:7-52              -------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: D:1-40 UniProt: 22-67   ---------------------------1.3   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2c  PDB: D:40-68      ---- Transcript 1 (2)
                  1qe6 D  1 SAKECRCQCIKTYSKPFHPKFIKELRVIESGPCCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 72
                                    10        20        30        40        50        60        70  

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: IL8 (55)
1aIL8-1qe6D01D:1-66
1bIL8-1qe6D02D:1-66
1cIL8-1qe6D03D:1-66
1dIL8-1qe6D04D:1-66

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IL8_HUMAN | P10145)
molecular function
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0005153    interleukin-8 receptor binding    Interacting selectively and non-covalently with the interleukin-8 receptor.
    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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0036499    PERK-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0044344    cellular response to fibroblast growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus.
    GO:0071347    cellular response to interleukin-1    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0050930    induction of positive chemotaxis    Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0045744    negative regulation of G-protein coupled receptor protein signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042119    neutrophil activation    The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0045091    regulation of single stranded viral RNA replication via double stranded DNA intermediate    Any process that modulates the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0002237    response to molecule of bacterial origin    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL8_HUMAN | P101451icw 1ikl 1ikm 1il8 1ilp 1ilq 1rod 2il8 3il8 4xdx 5d14

(-) Related Entries Specified in the PDB File

1icw MUTANT INTERLEUKIN-8 E38C/C50A
3il8 WILD-TYPE INTERLEUKIN-8 X-RAY