SMTL ID : 4fuc.1

Crystal Structure of the Urokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x 239: 6-[(Z)-AMINO(IMINO)METHYL]-N-[4-(AMINOMETHYL)PHENYL]-2-NAPHTHAMIDE(Non-covalent)

239.1: 21 residues within 4Å: Chain A: H.46, I.49, D.50, Y.87, H.94, D.192, S.193, C.194, Q.195, S.198, V.216, S.217, W.218, G.219, G.221, C.222, A.223, G.229, V.230, Y.231 Ligands: SIN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.46, A:Q.195, A:V.216 Hydrogen bonds: A:H.46, A:D.192, A:S.193, A:G.221 Water bridges: A:S.193 pi-Stacking: A:H.46

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 10 residues within 4Å: Chain A: V.30, C.31, H.46, C.47, Y.150, Q.195, G.196, D.197, S.198 Ligands: 239.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.46, A:G.196, A:S.198, A:S.198 Salt bridges: A:H.46

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

SO4.3: 5 residues within 4Å: Chain A: H.84, N.96, K.180, H.236, F.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.96 Salt bridges: A:K.180, A:H.236 SO4.4: 5 residues within 4Å: Chain A: H.95, N.96, T.178, K.180, M.181 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.178 Water bridges: A:N.96, A:N.96, A:N.96 Salt bridges: A:H.95, A:K.180 SO4.5: 4 residues within 4Å: Chain A: M.125, Y.126, R.233, H.236 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.233, A:R.233, A:H.236 Salt bridges: A:R.233, A:H.236 SO4.6: 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

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

ACT.7: 3 residues within 4Å: Chain A: H.164, T.178, T.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.179, A:T.179 Salt bridges: A:H.164

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: T.28, Y.29, L.66, Y.150 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.29, A:Y.150 Water bridges: A:T.28, A:Y.150 GOL.9: 3 residues within 4Å: Chain A: D.90, T.91, E.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.90, A:T.91, A:T.91 GOL.10: 4 residues within 4Å: Chain A: R.20, H.22, R.23, Y.51 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.20, A:R.20, A:H.22, A:R.23, A:Y.51 Water bridges: A:R.23, A:Y.51 GOL.11: 8 residues within 4Å: Chain A: Y.19, V.27, T.28, Y.29, L.66, N.67 Ligands: GOL.8, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.29, A:N.67 GOL.12: 5 residues within 4Å: Chain A: S.37, P.38, C.39, W.40, K.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.37, A:S.37, A:C.39, A:W.40 GOL.13: 3 residues within 4Å: Chain A: K.142, Y.148, Q.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.142, A:Q.195 Water bridges: A:Q.195 GOL.14: 9 residues within 4Å: Chain A: Y.19, V.27, I.58, Y.60, R.63, L.66, N.67, K.75 Ligands: GOL.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.60, A:Y.60, A:R.63, A:N.67 Water bridges: A:R.63, A:N.69, A:K.75 GOL.15: 2 residues within 4Å: Chain A: K.75, K.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75, A:K.106

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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