SMTL ID : 5lhq.1

The EGR-cmk 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 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0GJ: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide(Covalent)

0GJ.1: 17 residues within 4Å: Chain A: H.47, L.93, Y.95, D.193, S.194, C.195, K.196, G.197, D.198, S.199, V.217, S.218, W.219, G.220, G.222, G.230 Ligands: SO4.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.217 Hydrogen bonds: A:Y.95, A:S.194, A:G.197, A:D.198, A:S.199, A:S.218, A:G.220, A:G.220 Salt bridges: A:K.143, A:D.193, A:K.196

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

SO4.2: 5 residues within 4Å: Chain A: H.96, N.97, N.179, K.181 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.97, A:N.179 Water bridges: A:Y.87 Salt bridges: A:H.96, A:K.181 SO4.3: 4 residues within 4Å: Chain A: Q.167, Q.170, H.172, Y.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.167, A:Q.170, A:Y.173 Salt bridges: A:H.172 SO4.4: 4 residues within 4Å: Chain A: G.220, R.221, G.222 Ligands: 0GJ.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.222 Salt bridges: A:R.221 SO4.5: 2 residues within 4Å: Chain A: S.115, R.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.116 SO4.6: 2 residues within 4Å: Chain A: Y.180, R.234 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.234 SO4.7: 2 residues within 4Å: Chain A: N.206, G.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.206 SO4.10: 4 residues within 4Å: Chain B: P.88, V.131, S.132, S.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.132, B:S.133 SO4.11: 6 residues within 4Å: Chain A: S.107 Chain B: R.45, G.117, Y.118, G.119, W.123 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.119, B:M.120, A:S.107 Water bridges: B:R.45 Salt bridges: B:R.45 SO4.12: 2 residues within 4Å: Chain B: S.25, G.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 SO4.13: 2 residues within 4Å: Chain B: L.18, R.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.19 Water bridges: B:S.17, B:Q.82 SO4.14: 3 residues within 4Å: Chain B: S.52, S.53, S.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.52, B:S.53, B:S.53, B:S.54 Water bridges: B:G.56

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

EDO.8: 9 residues within 4Å: Chain A: Y.95, H.96, N.97, D.98, K.181, M.182, T.233, F.238 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.97, A:D.98, A:N.179, A:T.233 Water bridges: A:S.218 EDO.9: 2 residues within 4Å: Chain A: P.125, R.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.126

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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