SMTL ID : 8a7d.1

Partial dimer complex of PAPP-A and its inhibitor STC2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.644, S.646, H.656, E.703, E.705 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.644, A:S.646, A:E.703 NAG.2: 1 residues within 4Å: Chain A: N.399 No protein-ligand interaction detected (PLIP) NAG.3: 6 residues within 4Å: Chain A: C.343, D.344, P.345, N.348, H.354, C.359 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.345 Hydrogen bonds: A:H.354, A:C.359 NAG.4: 5 residues within 4Å: Chain A: D.282, N.321, S.323, L.324, I.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.323, A:S.323 NAG.5: 6 residues within 4Å: Chain A: S.264, R.267, Q.268, P.269, N.309, V.571 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.571 Hydrogen bonds: A:Q.268, A:N.309 NAG.6: 3 residues within 4Å: Chain A: P.511, F.513, N.520 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.513 Hydrogen bonds: A:N.520, A:N.523 NAG.7: 4 residues within 4Å: Chain A: K.736, N.744, Q.773, Y.775 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.1242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1242

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: L.444, H.481, H.485, H.491 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.481, A:H.485, A:H.491

8 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: K.337, D.340, N.342, D.344, D.355, D.358 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.337, A:D.344, A:D.355, A:D.355, A:D.358 CA.10: 4 residues within 4Å: Chain A: E.508, D.517, C.519, T.522 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.508, A:D.517, A:C.519, A:T.522, A:T.522 CA.11: 5 residues within 4Å: Chain A: V.375, C.376, D.377, C.380, D.388 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.377, A:D.388 CA.12: 5 residues within 4Å: Chain A: E.661, E.663, D.667, R.677, D.784 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.661, A:D.667, A:R.677, A:D.784, A:D.784 CA.13: 6 residues within 4Å: Chain A: Y.865, D.868, I.870, Q.872, E.877, D.880 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.865, A:D.868, A:I.870, A:E.877, A:D.880 CA.14: 5 residues within 4Å: Chain A: D.881, N.883, I.885, D.888, C.890 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.881, A:I.885, A:D.888, A:D.888, A:C.890 CA.15: 6 residues within 4Å: Chain A: H.912, D.915, V.917, E.919, E.922, D.929 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.912, A:D.915, A:V.917, A:E.919, A:E.922 CA.17: 6 residues within 4Å: Chain C: F.1480, D.1483, Y.1485, D.1487, D.1498, D.1501 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:F.1480, C:D.1487, C:D.1498, C:D.1498, C:D.1501

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobbero, S.D. et al., Structure of the proteolytic enzyme PAPP-A with the endogenous inhibitor stanniocalcin-2 reveals its inhibitory mechanism. Nat Commun (2022)

Release Date

2022-11-02

Peptides

Pappalysin-1: AC
Stanniocalcin-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
Q

B
P

Pappalysin-1

Stanniocalcin-2

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