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)
S.cerevisiae 2v3k 219 31 175-225 (27)
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 2p02 380 31 59-302 (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

References

Questions about particular knots? Contact Peter Virnau.

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