Believe It or Not!

From Proteopedia

Revision as of 10:02, 22 June 2022

A list of Useful, Useless or simply Interesting facts on Proteins, Structures and what's around them, automatically updated by OCA, the browser and database for structure and function.

The most common ...

• The most common Sources are Homo sapiens, present in 43,360 PDB structures and Escherichia coli, present in 11,043 PDB structures.
• The most common Ligand is GOL, present in 20,630 PDB structures (excluding SO4)
• The most common Space group is P 21 21, present in 32,728 PDB structures.

The most conspicuous ...

• The least popular experiment type is Solution Scattering used on 3 structures (1ntj, 1ntl, 1r70) over 191,871 ( 0.00%)
• The most popular experiment type is X-ray Diffraction used on 166,332 structures over 191,871 (86.69%)
• The structures with the most biomolecules are 2zzs, 4dx9 with 32 each and 5lhy with 30.
• The PDB structure with the most models is 2hyn, with 184 models.
• The PDB structures with the most related structures are 4b2b, 4b2c, 4b1t with 287 related structures each.
• The PDB structure with the most chains is 4v99 with 480 chains.
• The PDB structures with the longest chain are 4v5x, 4v5x with 7,249 amino acids (alpha carbons only) each.
• The PDB structures with the shortest chain (greater than one residue) are 1b2m, 1cwp, 1d53, 1ddl, 1dn8, 1ehl, 1f0v, 1i8m, 1ijs, 1kqs, 1lgc, 1m6a, 1n38, 1oup, 1pv4, 1pvo, 1q81, 1q82, 1rnb, 1vy6, 1xam, 279d, 2d7g, 2dwl, 2dwm, 2dwn, 2ht1, 2htt, 2ok0, 2pjr, 2vrt, 3er9, 3j0l, 3j0o, 3j0p, 3j0q, 3j5l, 3j9m, 3ngz, 3nma, 3ra4, 3ra9, 3rec, 3rtj, 3u2e, 3ucu, 3ucz, 3ud3, 3ud4, 3va0, 4a3g, 4a3j, 4a8k, 4afy, 4dy8, 4e60, 4ejt, 4g7o, 4jzu, 4jzv, 4lq3, 4nia, 4nku, 4ohy, 4oi0, 4oi1, 4oq8, 4oq9, 4pei, 4tzd, 4wti, 4wtj, 4wtk, 4wtl, 4wtm, 4x4n, 4x4r, 4x4t, 4x4t, 4x4u, 5f6c, 5jju, 5k77, 5kal, 5mmi, 5tgm, 5uh6, 5uh9 with 2 residues each.
• The PDB structure with the most amino acids is 3jb9 with 39,298 amino acids (alpha carbons only).
• The PDB structure with the largest number ALTLOC is 1zir with 22 alternate location.
• The PDB structures with the heaviest chain are 4v5x, 4v5x with 615,436.39 each.
• The PDB structures with the most ligands are 3wu2, 5b5e, 5b66, 5h2f, 5ws6 with 21 ligands each.
• The PDB structures with the largest number of distinct chemical elements are 3cpw, 3l4p, 3ow2, 5t5i, 5t61 with 12 elements each.
• The 10 most popular Chemical Elements, excluding C,O,S,P,H,Na,Cl,K are Zinc (Zn) on 12,593 PDB, Magnesium (Mg) on 12,137 PDB, Calcium (Ca) on 9,323 PDB, Selenium (Se) on 8,428 PDB, Iron (Fe) on 7,551 PDB, Fluorine (F) on 4,356 PDB, Manganese (Mn) on 2,868 PDB, Bromine (Br) on 1,462 PDB, Nickel (Ni) on 1,411 PDB and Copper (Cu) on 1,359 PDB.
• The most exotic Chemical Elements are Americium (Am 4zhg), Bismuth (Bi 4h0w), Californium (Cf 5kic), Curium (Cm 4zhf), Dysprosium (Dy 4ll7), Neon (Ne 2axt), Plutonium (Pu 4zhd), Scandium (Sc 3zi4), Titanium (Ti 5dyh) found in one PDB structure each.
• The PDB structure with the largest file is 4pth with 26,602,110 bytes (compressed).
• The PDB structure with the smallest file is 3rec with 2,999 bytes (compressed).
• The PDB structures with the most sources are 2wsc, 2wse and 2wsf with 6 sources each.
• There are 1,551 sources that occur in only a single entry. See Structures with Exotic Sources

Determination methods ...

• The PDB structure solved with Electron Crystallography with the best resolution is 6kj3 with 0.6 Å.
• The PDB structure solved with Electron Microscopy with the best resolution is 7a6a with 1.15 Å.
• The PDB structures solved with Fiber Diffraction with the best resolution are 1hgv, 1hgz, 1hh0 with 2.4 Å each.
• The PDB structure solved with Neutron Diffraction with the best resolution is 4ar3 with 1.05 Å.
• The PDB structure solved with Powder Diffraction with the best resolution is 1ja2 with 2.87 Å.
• The PDB structures solved with Solution Scattering with the best resolution are 1ntj, 1ntl, 1r70 with 30 Å each.
• The PDB structures solved with X-ray Diffraction with the best resolution are 3nir, 5d8v with 0.48 Å each.
• The mean resolution for PDB structures solved with Electron Crystallography is 2.94 ± 3.22 based on 185 structures
• The mean resolution for PDB structures solved with Electron Microscopy is 5.34 ± 5.16 based on 7,015 structures
• The mean resolution for PDB structures solved with Fiber Diffraction is 3.37 ± 0.7 based on 37 structures
• The mean resolution for PDB structures solved with Neutron Diffraction is 1.9 ± 0.35 based on 74 structures
• The mean resolution for PDB structures solved with Powder Diffraction is 3.07 ± 0.21 based on 6 structures
• The mean resolution for PDB structures solved with Solution Scattering is 30 ± 0 based on 3 structures
• The mean resolution for PDB structures solved with X-ray Diffraction is 2.13 ± 0.59 based on 166,332 structures
• The PDB structure solved with Electron Crystallography with the worst resolution is 2dfs with 24.0 Å.
• The PDB structures solved with Electron Microscopy with the worst resolution are 1m8q, 1mvw, 1o18, 1o19, 1o1a, 1o1b, 1o1c, 1o1d, 1o1e, 1o1f, 1o1g with 70.0 Å each.
• The PDB structures solved with Fiber Diffraction with the worst resolution are 3hqv, 3hr2 with 5.16 Å each.
• The PDB structure solved with Neutron Diffraction with the worst resolution is 1wqz with 3 Å.
• The PDB structure solved with Powder Diffraction with the worst resolution is 1xft with 3.35 Å.
• The PDB structures solved with Solution Scattering with the worst resolution are 1ntj, 1ntl, 1r70 with 30 Å each.
• The PDB structure solved with X-ray Diffraction with the worst resolution is 2tma with 15 Å.

Overall Statistics ...

• The mean PDB file is 192.5K ± 335.86K based on 129,506 files.
• There are 4 structure files with 12 citations (1dtq,1dtt,1het,3u87) and 1 structure file with 4 citations (11ba).

Updated by OCA on Wed Jun 22 13:02:45 2022

Notes

• 4tst is a useful PDB id for a non-existing structure *Search for this page with the word BelieveItOrNot -- all the words in the real title "Believe It Or Not!" are so common that they are ignored by the search index mechanism (see Help:Stop Words), so you will not succeed searching for the real title. This page is also linked to the Main Page.

See Also

• Atomic coordinate file
• Ligands
• NMR Ensembles of Models
• Protein Data Bank
• Resolution
• Standard Residues
• Unusual sequence numbering for "believe it or not" methods used to number some sequences.