SMTL ID : 2e3x.2 (2 other biounits)

Crystal structure of Russell's viper venom metalloproteinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.159, N.183 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: L.67, N.69, N.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.67, A:N.354, A:N.354 NAG.10: 1 residues within 4Å: Chain B: N.58 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.145, H.149, H.155 Ligands: GM6.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.145, A:H.149, A:H.155

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.14, D.96, C.200, N.203 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.14, A:D.96, A:D.96, A:C.200 CA.5: 6 residues within 4Å: Chain A: V.215, N.218, I.220, E.222, E.225, D.228 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.215, A:I.220, A:E.222, A:E.225, A:E.225 CA.6: 6 residues within 4Å: Chain A: R.272, D.279, V.280, E.282, D.294, Q.295 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.279, A:V.280, A:E.282, A:D.294, A:Q.295 CA.7: 2 residues within 4Å: Chain A: N.51, E.219 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.219, A:E.219 CA.11: 2 residues within 4Å: Chain B: E.83, G.87 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.83, B:G.87

1 x GM6: 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE(Non-covalent)

GM6.8: 17 residues within 4Å: Chain A: N.109, T.110, L.111, G.112, H.145, E.146, H.149, H.155, S.170, P.171, V.172, L.173 Chain C: Y.62, I.99, M.110, F.114 Ligands: ZN.3 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.172, A:L.173, C:I.99, C:F.114 Hydrogen bonds: A:N.109, A:L.111, A:G.112, A:G.112, A:P.171, A:L.173

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.9: 5 residues within 4Å: Chain C: N.23, T.25, D.26, C.112, N.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeda, S. et al., Crystal structure of RVV-X: an example of evolutionary gain of specificity by ADAM proteinases. Febs Lett. (2007)

Release Date

2007-12-11

Peptides

Coagulation factor X-activating enzyme heavy chain: A
Coagulation factor X-activating enzyme light chain 2: B
Coagulation factor X-activating enzyme light chain 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Coagulation factor X-activating enzyme heavy chain

Coagulation factor X-activating enzyme light chain 2

Coagulation factor X-activating enzyme light chain 1

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