SMTL ID : 7y5n.1

Structure of 1:1 PAPP-A.ProMBP complex(half map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-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: 6 residues within 4Å: Chain B: S.265, R.268, Q.269, P.270, Q.308, N.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.265

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

NAG.2: 5 residues within 4Å: Chain B: N.322, S.324, L.325, R.328, I.424 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.324, B:R.328 NAG.3: 4 residues within 4Å: Chain B: N.349, H.355, C.360, R.361 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.355, B:H.355, B:R.361 NAG.4: 3 residues within 4Å: Chain B: R.327, N.400, Q.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.403 NAG.5: 1 residues within 4Å: Chain B: N.521 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: N.645, S.647 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.647 NAG.7: 2 residues within 4Å: Chain B: K.737, N.745 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.737, B:N.745 NAG.8: 1 residues within 4Å: Chain B: N.946 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: L.824, N.825 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.825 NAG.11: 3 residues within 4Å: Chain B: P.537, N.539, D.540 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.537 Hydrogen bonds: B:D.540, B:D.540, B:D.540 NAG.19: 7 residues within 4Å: Chain C: E.1141, N.1142, Y.1166, A.1199, C.1200, E.1201, P.1202 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.1141, C:A.1199 Hydrogen bonds: C:E.1141, C:C.1200

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain B: L.445, H.482, H.486, H.492 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.482, B:H.486, B:H.492

7 x CA: CALCIUM ION(Non-covalent)

CA.12: 4 residues within 4Å: Chain B: A.663, D.668, R.678, D.785 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.668, B:R.678, B:D.785, B:D.785 CA.13: 5 residues within 4Å: Chain B: N.374, V.376, D.378, D.389, E.392 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.376, B:D.389, B:E.392 CA.14: 6 residues within 4Å: Chain B: Y.866, D.869, I.871, Q.873, E.878, D.881 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:Y.866, B:D.869, B:I.871, B:E.878, B:E.878 CA.15: 4 residues within 4Å: Chain B: E.509, D.518, C.520, T.523 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.509, B:D.518, B:C.520, B:T.523, B:T.523 CA.16: 5 residues within 4Å: Chain B: H.913, D.916, V.918, E.923, D.930 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.913, B:V.918, B:E.923, B:D.930 CA.17: 6 residues within 4Å: Chain B: K.338, I.339, D.341, N.343, D.345, D.356 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:K.338, B:D.341, B:N.343, B:D.345, B:D.356 CA.18: 3 residues within 4Å: Chain B: N.884, I.886, C.891 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.886, B:C.891

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, Q. et al., Structural insights into the covalent regulation of PAPP-A activity by proMBP and STC2. Cell Discov (2022)

Release Date

2023-01-11

Peptides

Bone marrow proteoglycan: A
Pappalysin-1: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Bone marrow proteoglycan

Pappalysin-1

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