SMTL ID : 6qig.1

Metalloproteinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain B: E.1, Q.3, S.25, G.26 Chain C: N.68, S.71 Ligands: MAN.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.3, B:E.1, B:E.1, B:Q.3, B:G.26

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

NAG-NAG.2: 4 residues within 4Å: Chain C: R.466, G.472, D.473, N.474 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.589 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.3: 4 residues within 4Å: Chain C: N.536, R.551, V.552 Ligands: PEG.25 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain C: T.499, P.500, N.501, Q.601 No protein-ligand interaction detected (PLIP)

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: W.163 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: S.122, E.123 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: K.19 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: D.1 Chain B: D.62, K.65 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain C: T.136 Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain A: N.212, E.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.213 PEG.10: 3 residues within 4Å: Chain A: T.126, G.128, K.183 No protein-ligand interaction detected (PLIP) PEG.14: 3 residues within 4Å: Chain B: G.54, G.55, T.56 No protein-ligand interaction detected (PLIP) PEG.15: 7 residues within 4Å: Chain B: Q.39, T.40, K.43, A.92, T.120, V.121, T.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.120 PEG.23: 6 residues within 4Å: Chain C: D.21, R.24, Y.226, E.231, N.334, N.335 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.21, C:N.335 PEG.24: 3 residues within 4Å: Chain C: V.505, R.566, I.567 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.566, C:I.567 PEG.25: 4 residues within 4Å: Chain C: R.561, L.562, E.564 Ligands: NAG-NAG-BMA-MAN.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.561, C:E.564 PEG.27: 4 residues within 4Å: Chain C: E.585, E.586, Y.587, G.588 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Y.32, Y.91, R.93 Chain B: A.101, D.109 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.91, A:R.93, A:R.93, A:R.93, B:D.109 Water bridges: B:D.109 GOL.26: 2 residues within 4Å: Chain C: D.594, T.596 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.11: 2 residues within 4Å: Chain B: Q.3 Ligands: NAG-NAG-BMA.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.1, B:E.1, B:Q.3

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.16: 2 residues within 4Å: Chain C: S.321, C.322 No protein-ligand interaction detected (PLIP)

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

NAG.17: 2 residues within 4Å: Chain C: A.62, N.64 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 3 residues within 4Å: Chain C: H.146, H.150, H.156 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.146, C:H.150, C:H.156, H2O.6

3 x CA: CALCIUM ION(Non-covalent)

CA.19: 5 residues within 4Å: Chain C: D.104, L.105, R.112, V.114, E.134 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.104, C:L.105, C:R.112, C:V.114, H2O.5 CA.20: 6 residues within 4Å: Chain C: E.5, D.88, D.95, C.203, D.206 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.5, C:D.88, C:D.95, C:C.203, C:D.206 CA.21: 4 residues within 4Å: Chain C: E.5, D.88, D.206 Ligands: CA.20 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.5, C:D.88, C:D.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petri, A. et al., Crystal structure and substrate-induced activation of ADAMTS13. Nat Commun (2019)

Release Date

2019-09-04

Peptides

Antibody Light Chain: A
Antibody Heavy Chain: B
A disintegrin and metalloproteinase with thrombospondin motifs 13: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

Antibody Light Chain

Antibody Heavy Chain

A disintegrin and metalloproteinase with thrombospondin motifs 13