SMTL ID : 5lhn.1

The catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: Q.167, Q.170, H.172, Y.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167, A:Y.173 Salt bridges: A:H.172 SO4.2: 2 residues within 4Å: Chain A: S.115, R.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.116 Salt bridges: A:R.116 SO4.3: 4 residues within 4Å: Chain A: H.96, N.97, N.179, K.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.97, A:N.179 Salt bridges: A:H.96, A:K.181 SO4.5: 2 residues within 4Å: Chain B: L.18, R.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.19 SO4.6: 2 residues within 4Å: Chain B: S.25, G.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 SO4.7: 5 residues within 4Å: Chain B: S.52, S.54, G.56, S.57, A.107 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.52, B:S.54, B:G.55, B:G.56, B:S.57 Water bridges: B:S.54, B:S.54 SO4.8: 3 residues within 4Å: Chain B: P.88, S.132, S.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.132, B:S.133

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: R.126 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: S.107 Chain B: R.45, Y.118, G.119, W.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.45, B:R.45, B:G.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kromann-Hansen, T. et al., Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep (2017)

Release Date

2017-06-28

Peptides

Urokinase-type plasminogen activator: A
Camelid-Derived Antibody Fragment Nb7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator

Camelid-Derived Antibody Fragment Nb7

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