SMTL ID : 4fub.1

Crystal Structure of the Urokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 4UP: 6-[(2S,3S)-3-phenyloxiran-2-yl]naphthalene-2-carboximidamide(Non-covalent)

4UP.1: 13 residues within 4Å: Chain A: H.46, H.94, D.192, S.193, Q.195, S.198, V.216, W.218, G.219, G.221, C.222, G.229 Ligands: SIN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.195, A:V.216 Hydrogen bonds: A:D.192, A:D.192, A:S.193 Water bridges: A:V.230 pi-Stacking: A:H.46

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

SO4.2: 4 residues within 4Å: Chain A: H.95, T.178, K.180, M.181 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.96, A:N.96 Salt bridges: A:H.95, A:K.180

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 7 residues within 4Å: Chain A: V.30, C.31, H.46, Q.195, G.196, S.198 Ligands: 4UP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.195, A:G.196, A:S.198, A:S.198 Salt bridges: A:H.46

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: T.28, Y.29, Y.150 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.29 Water bridges: A:Y.150, A:Y.150 GOL.5: 5 residues within 4Å: Chain A: V.27, T.28, Y.29, N.67 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.27, A:Y.29, A:N.67, A:N.67 GOL.6: 5 residues within 4Å: Chain A: K.142, D.147, Y.148, Q.195 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.142, A:Q.195, A:Q.195 GOL.7: 7 residues within 4Å: Chain A: K.142, S.145, C.194, Q.195, G.221, C.222 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.142, A:S.145, A:S.145 Water bridges: A:C.222 GOL.8: 2 residues within 4Å: Chain A: K.75, K.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.75 Water bridges: A:K.75, A:K.75, A:K.106, A:K.106 GOL.10: 4 residues within 4Å: Chain A: R.20, H.22, R.23, Y.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.20, A:R.20, A:H.22, A:R.23, A:Y.51

1 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.9: 7 residues within 4Å: Chain A: S.37, P.38, C.39, W.40, K.102, T.245, K.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.39

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 3 residues within 4Å: Chain A: Y.126, R.233, H.236 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.126 Water bridges: A:R.233 Salt bridges: A:R.233, A:H.236 ACT.12: 2 residues within 4Å: Chain A: K.180, H.236 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.180, A:H.236 ACT.13: 2 residues within 4Å: Chain A: T.178, T.179 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.179 Hydrogen bonds: A:T.179 ACT.14: 2 residues within 4Å: Chain A: P.52, L.81 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.81 ACT.15: 3 residues within 4Å: Chain A: R.23, G.24, G.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, Y.N. et al., Crystal Structure of the Urokinase. to be published

Release Date

2012-08-22

Peptides

Urokinase-type plasminogen activator: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Urokinase-type plasminogen activator

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