SMTL ID : 2fd6.1 (1 other biounit)

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain D: N.53, V.71 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.53, D:V.71, D:V.71 Water bridges: D:N.53

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain D: N.173 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: D.2, H.19, H.31 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:D.2 Salt bridges: A:H.19, A:H.31 Water bridges: D:T.9, D:T.9, D:T.9

3 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.4: 5 residues within 4Å: Chain B: D.1, I.2, Q.89, N.91, P.93 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.2 Hydrogen bonds: B:D.1, B:D.1 Water bridges: B:N.91 ETX.6: 5 residues within 4Å: Chain B: Y.92 Chain C: E.59, K.65 Chain D: G.192, Q.194 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.92, D:Q.194 ETX.7: 3 residues within 4Å: Chain C: K.23, S.76, T.78 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.76, C:T.78 Water bridges: C:K.23

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

EDO.5: 5 residues within 4Å: Chain B: K.44, P.45, W.46, A.54, S.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.45 EDO.8: 5 residues within 4Å: Chain C: K.19, T.71, A.72, D.73, Y.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.19, C:T.71

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 8 residues within 4Å: Chain C: N.31, F.32, Y.33, W.99, W.103 Chain D: L.188, P.219 Ligands: PG4.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.33

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.10: 4 residues within 4Å: Chain D: N.201, T.203, H.204, S.236 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.201 Hydrogen bonds: D:N.201, D:T.203, D:T.203 Salt bridges: D:H.204

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 11 residues within 4Å: Chain C: N.31, F.52, H.53, D.56, N.57 Chain D: P.219, N.221, Q.222, T.244, A.245 Ligands: PGE.9 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.222, D:A.245, C:D.56, C:N.57 Water bridges: D:S.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huai, Q. et al., Structure of human urokinase plasminogen activator in complex with its receptor. Science (2006)

Release Date

2006-02-21

Peptides

Urokinase-type plasminogen activator: A
L chain of Fab of ATN-615 anti-uPAR antibody: B
H chain of Fab of ATN-615 anti-uPAR antibody: C
Urokinase plasminogen activator surface receptor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

D
U

Urokinase-type plasminogen activator

L chain of Fab of ATN-615 anti-uPAR antibody

H chain of Fab of ATN-615 anti-uPAR antibody

Urokinase plasminogen activator surface receptor

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