SMTL ID : 5lhp.1

The p-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.47, K.196, G.197, S.199 Ligands: PBZ.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.197, A:S.199, A:S.199 Salt bridges: A:H.47, A:K.196 SO4.2: 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 SO4.3: 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 SO4.4: 2 residues within 4Å: Chain A: N.206, G.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.206 SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: E.146, G.220, R.221, G.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.222 SO4.7: 2 residues within 4Å: Chain A: P.125, R.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126, A:R.126 SO4.8: 2 residues within 4Å: Chain A: K.23, G.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.24 SO4.12: 2 residues within 4Å: Chain B: L.18, R.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.19 SO4.13: 2 residues within 4Å: Chain B: S.25, G.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 SO4.14: 3 residues within 4Å: Chain B: A.40, P.41, G.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.42 SO4.15: 3 residues within 4Å: Chain B: S.52, S.53, S.54 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.52, B:S.53, B:S.54 Water bridges: B:S.53, B:S.53, B:G.56 SO4.16: 3 residues within 4Å: Chain B: P.88, S.132, S.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.133 SO4.17: 4 residues within 4Å: Chain B: T.58, N.59, Y.60, K.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.60 Water bridges: B:N.59, B:Q.110 Salt bridges: B:K.65

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

EDO.9: 8 residues within 4Å: Chain A: Y.95, H.96, N.97, D.98, K.181, M.182, T.233, F.238 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.96, A:N.97, A:D.98, A:N.179, A:T.233 EDO.10: 4 residues within 4Å: Chain A: F.132, H.165, Y.180, R.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.234 Water bridges: A:H.165

1 x PBZ: P-AMINO BENZAMIDINE(Non-covalent)

PBZ.11: 11 residues within 4Å: Chain A: D.193, S.194, S.199, V.217, S.218, W.219, G.220, G.222, C.223, G.230 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.217 Hydrogen bonds: A:D.193, A:S.194, A:S.199, A:G.222

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator

Camelid-Derived Antibody Fragment

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