spacer
spacer

ProFunc results for 1mbn

3D structure
Jmol   RasMol
Header details

Structure:
THE STEREOCHEMISTRY OF THE PROTEIN MYOGLOBIN

Source:
Physeter catodon. Sperm whale. Organism_taxid: 9755

Date:
05 Apr 73

Author(s):
H.C.Watson,J.C.Kendrew

Resolution:
2.000Å       R-factor: -9.900      

Summary of predicted function

+ Protein name terms
myoglobin (319.22) sperm whale (124.28) sperm whale myoglobin (109.18) gn=mb (40.50) carbonmonoxy (37.41) horse (35.00) horse heart (33.01) laser (28.74)

+ Gene Ontology (GO) terms
Cellular component: cytoplasm (27.93) cell (27.93) cell part (27.93) intracellular (27.93)
Biological process: transport (416.18) oxygen transport (416.18) establishment of localization (416.18) localization (416.18)
Biochemical function: oxygen transporter activity (417.03) transporter activity (417.03) substrate\-specific transporter activity (417.03) oxygen binding (416.18)
The protein names and GO terms above are the most common terms found in the hits obtained from the analyses below. Each term's score (based on the number of times it occurs independently) is given in brackets. Click on the plus icons for a complete breakdown of which programs, and further, which hits the terms came from.

ProFunc results

Sequence motifs

InterPro scan for sequence motifs. Chain A

6 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs

  Type Motif Name
1. SUPERFAMILY SSF46458
2. Pfam PF00042 Globin
3. ??? PR00613x5 Myoglobin signature
4. ProSiteProfiles PS01033 Globin family profile.
5. PANTHER PTHR11442:SF5
... plus others

Matches to existing PDB structures

Sequence search vs existing PDB entries. Chain A

399 matching sequences found by FASTA search

  PDB code E-value %-tage id Overlap Name
1. 104m(A) 7e-64 100.000 153 Sperm whale myoglobin n-butyl isocyanide at ph 7.0
2. 105m(A) 7e-64 100.000 153 Sperm whale myoglobin n-butyl isocyanide at ph 9.0
3. 1ajg(A) 7e-64 100.000 153 Carbonmonoxy myoglobin at 40 k
4. 1ajh(A) 7e-64 100.000 153 Photoproduct of carbonmonoxy myoglobin at 40 k
5. 1bvc(A) 7e-64 100.000 153 Structure of a biliverdin apomyoglobin complex (form d) at 118 k
... plus others

Sequence search

BLAST search vs Uniprot. Chain A

50 matching sequences found by BLAST search

  Ref. no. E-value %-tage id Overlap Name
1. MYG_PHYCD 9e-96 100.000 153 P02185 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2
2. MYG_KOGSI 7e-93 96.732 153 P02184 Myoglobin OS=Kogia sima GN=MB PE=1 SV=2
3. R9RZK8_BALMY 1e-90 93.464 153 R9RZK8 Myoglobin OS=Balaena mysticetus GN=Mb PE=2 SV=1
4. MYG_ESCGI 3e-89 92.810 153 P02177 Myoglobin OS=Eschrichtius gibbosus GN=MB PE=1 SV=2
5. R9RY75_MONMO 1e-88 92.105 152 R9RY75 Myoglobin OS=Monodon monoceros GN=Mb PE=2 SV=1
... plus others

Residue conservation analysis

Conservation mapped onto 3D structure.

 

Gene neighbours

Neighbouring genes on genome. Chain A

No genome locations found for any homologues.

Matching folds detected by SSM

Matching folds. Chain A

10846 significant structural matches

  Q-score Rmsd No. SSE Z-score PDB Name
1. 0.977 0.46Å 8 13.2 2mb5 Hydration in protein crystals. A neutron diffraction analysi carbonmonoxymyoglobin
2. 0.977 0.46Å 7 13.0 1cq2 Neutron struture of fully deuterated sperm whale myoglobin a angstrom
3. 0.976 0.47Å 7 13.2 1bzr Atomic resolution crystal structure analysis of native deoxy and co myoglobin from sperm whale at room temperature
4. 0.974 0.49Å 7 13.2 1bz6 Atomic resolution crystal structure aquomet-myoglobin from sperm whale at room temperature
5. 0.974 0.49Å 8 13.4 2zt0 Carbonmonoxy sperm whale myoglobin at 100 k: laser on [750 min]
... plus others

Nest analysis

Nest analysis. Chain A

2 nests located in the structure

  Score No.
resid.
Ave.
access-
ibility
Cleft Ave.
conser-
vation
Residues
1. 2.000 3 0.00 3 1.000 His97(A), Lys98(A), Ile99(A)
2. 0.954 3 0.00 - 0.954 Leu149(A), Gly150(A), Tyr151(A)

Cleft analysis

Surface clefts.

 

3D functional template searches

Enzyme active site templates.

No hits obtained from any of the 584 enzyme active site templates.

Ligand-binding templates.

20 significant hits out of 94055 ligand-binding templates.

  Score Template PDB Name
1. 780.000 HEMb0089 1a6k Aquomet-myoglobin, atomic resolution
Het Group HEM
2. 680.000 HEMb0026 110m Sperm whale myoglobin d122n methyl isocyanide at ph 9.0
Het Group HEM
3. 677.500 HEMb5693 2v1f Crystal structure of radiation-induced myoglobin compound ii - intermediate h at ph 8.7
Het Group HEM
4. 672.000 HEMb2607 1myf Solution structure of carbonmonoxy myoglobin determined from nmr distance and chemical shift constraints
Het Group HEM
5. 670.312 HEMb4984 2g0r Unphotolyzed co-bound l29f myoglobin
Het Group HEM
... plus others

DNA-binding templates.

No hits obtained from any of the 5320 DNA-binding templates.

Reverse template comparison vs structures in PDB.

20 significant hits out of 308 auto-generated templates.

  Score Template PDB Name
1. 760.000 TMP00132 1a6m Oxy-myoglobin, atomic resolution
2. 760.000 TMP00132 1h1x Sperm whale myoglobin mutant t67r s92d
3. 760.000 TMP00132 1mcy Sperm whale myoglobin (mutant with initiator met and with hi replaced by gln, leu 29 replaced by phe
4. 760.000 TMP00132 2ekt Crystal structure of myoglobin reconstituted with 6-methyl-6 depropionatehemin
5. 760.000 TMP00132 1naz Structure of microgravity-grown oxidized myoglobin mutant yqr (iss8a)
... plus others

Key

In the summaries above, the hits are coloured according to their likelihood of being correct as follows: certain matches, probable matches, possible matches, and long shots. If the reliability of a hit is unknown, it is shown in navy blue.

Generated on Thu 24 Apr 2014 spacer

spacer