SMTL ID : 8a7e.1

PAPP-A dimer in complex with its inhibitor STC2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: L.444, H.481, H.485, H.491, Y.557 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.481, B:H.485, B:H.491, B:Y.557 ZN.10: 5 residues within 4Å: Chain D: L.444, H.481, H.485, H.491, Y.557 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.481, D:H.485, D:H.491

16 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain B: K.337, I.338, G.339, D.340, N.342, D.344, D.355, D.358 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.340, B:D.340, B:D.344, B:D.355, B:D.358 CA.3: 7 residues within 4Å: Chain B: F.1480, D.1483, Y.1485, D.1487, N.1490, D.1498, D.1501 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.1480, B:D.1483, B:Y.1485, B:D.1498, B:D.1498 CA.4: 6 residues within 4Å: Chain B: E.508, P.511, S.512, D.517, C.519, T.522 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.508, B:D.517, B:C.519, B:T.522, B:T.522 CA.5: 7 residues within 4Å: Chain B: K.370, N.373, V.375, D.377, C.380, D.388, E.391 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:K.370, B:V.375, B:D.377, B:D.388, B:D.388 CA.6: 5 residues within 4Å: Chain B: K.454, E.661, D.667, R.677, D.784 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.661, B:D.667, B:D.667, B:R.677, B:D.784 CA.7: 8 residues within 4Å: Chain B: Y.865, C.866, G.867, D.868, I.870, Q.872, E.877, D.880 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.865, B:E.877, B:E.877, B:D.880 CA.8: 6 residues within 4Å: Chain B: D.881, N.883, K.884, I.885, D.888, C.890 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.881, B:N.883, B:I.885, B:D.888 CA.9: 7 residues within 4Å: Chain B: H.912, D.913, G.914, D.915, V.917, E.922, D.929 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.912, B:D.915, B:V.917, B:E.922, B:D.929 CA.11: 6 residues within 4Å: Chain D: H.912, D.915, V.917, E.919, E.922, D.929 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.912, D:D.915, D:V.917, D:E.922, D:E.922 CA.12: 5 residues within 4Å: Chain D: D.881, N.883, K.884, I.885, D.888 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.881, D:N.883, D:I.885, D:D.888 CA.13: 9 residues within 4Å: Chain D: Y.865, C.866, G.867, D.868, I.870, Q.872, E.877, D.880, C.894 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:Y.865, D:E.877, D:E.877, D:D.880 CA.14: 5 residues within 4Å: Chain D: K.454, E.661, D.667, R.677, D.784 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.661, D:D.667, D:R.677, D:D.784 CA.15: 7 residues within 4Å: Chain D: K.370, N.373, V.375, D.377, C.380, D.388, E.391 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:K.370, D:V.375, D:D.377, D:D.388, D:D.388 CA.16: 6 residues within 4Å: Chain D: E.508, P.511, S.512, D.517, C.519, T.522 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.508, D:D.517, D:C.519, D:T.522, D:T.522 CA.17: 7 residues within 4Å: Chain D: F.1480, D.1483, Y.1485, D.1487, N.1490, D.1498, D.1501 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:F.1480, D:D.1483, D:Y.1485, D:D.1498, D:D.1498 CA.18: 8 residues within 4Å: Chain D: K.337, I.338, G.339, D.340, N.342, D.344, D.355, D.358 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.340, D:D.344, D:D.355, D:D.355, D:D.358

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

Stanniocalcin-2: AC
Pappalysin-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

C
A

B
C

D
Q

Stanniocalcin-2

Pappalysin-1

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