1uex

X-ray diffraction
2.85Å resolution

Crystal structure of von Willebrand Factor A1 domain complexed with snake venom bitiscetin

Released:

Function and Biology Details

Reactions catalysed:
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
dUTP + H(2)O = dUMP + diphosphate
D-glycero-beta-D-manno-heptose 1-phosphate + ATP = ADP-D-glycero-beta-D-manno-heptose + diphosphate
Beta-nicotinate D-ribonucleotide + diphosphate + CO(2) = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
4a-hydroxytetrahydrobiopterin = 6,7-dihydrobiopterin + H(2)O
ATP = 3',5'-cyclic AMP + diphosphate
GTP + H(2)O = GDP + phosphate
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO(2)
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Cleavage of peptide bonds with very broad specificity.
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
L-asparagine + H(2)O = L-aspartate + NH(3)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
2-lysophosphatidylcholine + H(2)O = glycerophosphocholine + a carboxylate
A phenyl acetate + H(2)O = a phenol + acetate
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
ATP + shikimate = ADP + shikimate 3-phosphate
GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
NTP + H(2)O = NDP + phosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Oleoyl-[acyl-carrier-protein] + H(2)O = [acyl-carrier-protein] + oleate
[Biotin carboxyl-carrier protein]-N(6)-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N(6)-biotinyl-L-lysine + malonyl-CoA
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate
A chalcone = a flavanone
A beta-lactam + H(2)O = a substituted beta-amino acid
2-carboxy-2,5-dihydro-5-oxofuran-2-acetate = cis,cis-butadiene-1,2,4-tricarboxylate
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
RX + glutathione = HX + R-S-glutathione
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
Preferential cleavage of -Tyr(16)-|-Leu- and -Phe(25)-|-Tyr-bonds of oxidized insulin B chain. Also acts on other substrates of less than 7 kDa such as insulin and glucagon.
Peptidylproline (omega=180) = peptidylproline (omega=0)
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
2-phosphoglycolate + H(2)O = glycolate + phosphate
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
Acetyl-CoA + phosphate = CoA + acetyl phosphate
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
ATP + NAD(+) = ADP + NADP(+)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Acetyl-CoA + 3-methyl-2-oxobutanoate + H(2)O = (2S)-2-isopropylmalate + CoA
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Creatinine + H(2)O = creatine
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
((1->2)-beta-D-glucosyl)(n) + H(2)O = sophorose + ((1->2)-beta-D-glucosyl)(n-2)
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Palmitoyl-CoA + H(2)O = CoA + palmitate
AMP + H(2)O = D-ribose 5-phosphate + adenine
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
NADPH + NAD(+) + H(+)(Side 1) = NADP(+) + H(+)(Side 2) + NADH
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
ATP + a protein = ADP + a phosphoprotein
1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-C-(3-indolyl)-glycerol 3-phosphate + CO(2) + H(2)O
IMP + H(2)O = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + NAD(+) = 3-alpha,12-alpha-dihydroxy-7-oxo-5-beta-cholanate + NADH
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
ATP-dependent cleavage of peptide bonds with broad specificity.
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
(1a) L-tyrosine + 1/2 O(2) = L-dopa
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide = tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
5,10-methylenetetrahydrofolate + dUMP + NADPH = dTMP + tetrahydrofolate + NADP(+)
Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O-(1-carboxyvinyl)-3-phosphoshikimate
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
L-arginine + H(2)O = L-ornithine + urea
D-glyceraldehyde 3-phosphate = glycerone phosphate
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
An aldehyde + H(2)O + 2 oxidized ferredoxin = a carboxylate + 2 H(+) + 2 reduced ferredoxin
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
D-galactosyl-N-acylsphingosine + H(2)O = D-galactose + N-acylsphingosine
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
ATP + thymidine = ADP + thymidine 5'-phosphate
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
An ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO(2) + a holo-[acyl-carrier protein]
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
NAD(P)H + O(2) = NAD(P)(+) + H(2)O(2)
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + a UDP-3-O-((3R)-hydroxyacyl)-alpha-D-glucosamine = a UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevin (also known as neuronal vesicle-associated membrane protein, VAMP), synaptosome-associated protein of 25 kDa (SNAP25) or syntaxin. No detected action on small molecule substrates.
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
Release of N-terminal proline from a peptide.
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Prephenate = phenylpyruvate + H(2)O + CO(2)
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
L-aspartate = D-aspartate
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
Succinate semialdehyde + NAD(P)(+) + H(2)O = succinate + NAD(P)H
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
Adenosine + H(2)O = inosine + NH(3)
Beta-D-ribopyranose = beta-D-ribofuranose
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
3-dehydroquinate = 3-dehydroshikimate + H(2)O
ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu)
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Snaclec bitiscetin subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 131 amino acids
Theoretical weight: 14.95 KDa
Source organism: Bitis arietans
UniProt:
  • Canonical: Q7LZK5 (Residues: 1-131; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Snaclec bitiscetin subunit beta Chain: B
Molecule details ›
Chain: B
Length: 125 amino acids
Theoretical weight: 14.82 KDa
Source organism: Bitis arietans
UniProt:
  • Canonical: Q7LZK8 (Residues: 1-125; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
von Willebrand factor Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 23.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04275 (Residues: 1260-1468; Coverage: 8%)
Gene names: F8VWF, VWF
Sequence domains: von Willebrand factor type A domain
Structure domains: von Willebrand factor, type A domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6B
Spacegroup: P43
Unit cell:
a: 89.282Å b: 89.282Å c: 53.394Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.276
Expression system: Escherichia coli BL21(DE3)