Protein Knots
The knot server allows the user to check pdb entries or uploaded structures for knots and to visualize them. The size of a knot is determined by deleting amino acids from both ends. This procedure is, however, not perfect and the resulting size should only be treated as a guideline.

Please enter pdb id (e.g. 1v2x):

Or upload file (pdb or mmCIF):



List of known knots

Protein Species PDB code Length Knot Knotted core
YbeA-like E.coli 1ns5 153 31 69-121 (32)
T.maritima 1o6d 147 31 68-117 (30)
S.aureus 1vh0 157 31 73-126 (31)
B.subtilis 1to0 148 31 73-125 (32)
tRNA(m1G37)-methyltransferase TrmD H.influenza 1uaj 241 31 85-130 (92)
E.coli 1p9p 235 31 90-130 (89)
SpoU-like RNA 2'-O ribose mtf. T.thermophilus 1v2x 191 31 96-140 (51)
H.influenza 1j85 156 31 77-114 (42)
T.thermophilus 1ipa 258 31 190-234 (29)
E.coli 1gz0 242 31 173-215 (28)
A. aeolicus 1zjr 197 31 100-144 (58)
S. viridochromog. 1x7p 267 31 209-251 (31)
YggJ C-terminal domain-like H.influenza 1nxz 246 31 166-217 (30)
B.subtilis 1vhk 235 31 168-226 (27) 1
T.thermophilus 1v6z 227 31 104-203 (25) 3
Hypothetical protein MTH1 (MT0001) A.M. thermoautotr. 1k3r 262 31 48-234 (28)
 
Carbonic Anhydrases:  
Carbonic Anhydrase N. gonorrhoeae 1kop 223 31 39-226 (0)
Carbonic Anhydrase I H.sapiens 1hcb 258 31 29-256 (2)
Carbonic Anhydrase II H.sapiens 1lug 259 31 31-257 (3)
Bos Taurus 1v9e 259 31 32-256 (3)
Dunaliella salina 1y7w 274 31 39-272 (4)
Carbonic Anhydrase III Rattus norv. 1flj 259 31 31-258 (3)
H. sapiens 1z93 263 31 31-258 (9)
Carbonic Anhydrase IV H.sapiens 1znc 262 31 31-258 (1)
Carbonic Anhydrase V Mus musculus 1keq 238 31 31-258 (4)
Carbonic Anhydrase VII H.sapiens 1jd0 260 31 31-258 (3)
Carbonic Anhydrase XIV Mus Musculus 1rj6 259 31 31-258 (2)
 
Miscellaneous:  
Ubiquitin Hydrolase UCH-L3 H.sapiens 1xd3 229 52 13-212 (12) 4
S.cerevisiae (synth.) 1cmx 214 31 14-228 (6) 4,1
Ubiquitin Hydrolase UCH-L1 H.sapiens 2etl 219 52 10-216 (13)
S-adenosylmethionine synthetase E.coli 1fug 383 31 33-260 (32)
rattus norv. 1qm4 368 31 46-281 (29) 1
H. sapiens 2hj2 380 31 37-280 (21)
Class II ketol-acid reductoisomerase Spinacia oleracea 1yve 513 41 321-533 (62)
E.coli 1yrl 487 41 222-437 (52) 2
Transcarbamylase B.fragilis 1js1 324 31 169-267 (57)
X.campestris 1yh0 328 31 173-277 (57) 2
Methyltransferase H.sapiens 2ha8 159 31 103-148 (30)
P. gingivalis 2i6d 231 31 177-223 (9)


How we define knots

Mathematically, knots are only well defined in closed loops. However, the ends of proteins are usually located on the surface and can be connected unambiguously. A thus connected loop can be tested for knots with the Alexander polynomial.

In the course of our investigations we came up with a number of stringent criteria which a knotted structure should fulfill:

  1. The Alexander polynomial should yield a knot
  2. There should not be any gaps in the structure
  3. The knot should prevail if two amino acids are removed from each end. (This prevents "shallow knots" and knots which only appear due to our closure)

Unfortunately, there are many incomplete structures with gaps. If the structure is incomplete a knot should be present in at least one fragment and the structure which results when gaps are bridged with straight lines.

References

Virnau P, Mirny LA and Kardar M. Intricate knots in proteins: function and evolution. PLoS Comput Biol. 2006 Sep 15;2(9):e122. Epub 2006 Jul 28.
Mirny lab webpage

Questions about particular knots? Contact Peter Virnau.

Examples of different knot types:

Evolutionary origin:

Structures of Transcarbamylase from X. campestris with a Trefoil Knot and from Human without a Knot