SMTL ID : 1ywh.3 (2 other biounits)

crystal structure of urokinase plasminogen activator receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-4-mer

Ligands

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

NAG-FUC.1: 6 residues within 4Å: Chain A: N.52, V.69, R.83, V.85, S.117, E.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.83, A:V.85, A:S.117, A:S.117, A:N.52 NAG-FUC.3: 5 residues within 4Å: Chain A: T.226, G.227, T.228, N.233, H.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.226 Hydrogen bonds: A:N.233 NAG-FUC.6: 4 residues within 4Å: Chain E: N.52, V.69, S.117, E.119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.117, E:S.117, E:N.52 NAG-FUC.9: 4 residues within 4Å: Chain G: N.52, V.69, S.117, E.119 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.117, G:S.117

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 3 residues within 4Å: Chain A: I.130, N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain C: N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 2 residues within 4Å: Chain E: N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 3 residues within 4Å: Chain G: I.130, N.162, F.211 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 4 residues within 4Å: Chain C: N.52, S.117, P.118, E.119 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.119

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.8: 2 residues within 4Å: Chain E: P.154, N.172 No protein-ligand interaction detected (PLIP)

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

NAG.11: 1 residues within 4Å: Chain A: N.172 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain C: N.172 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain C: N.233, H.260 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain E: T.228, N.233, H.260 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain G: N.172 No protein-ligand interaction detected (PLIP)

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

SO4.12: 2 residues within 4Å: Chain A: R.13 Chain G: K.7 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Salt bridges: G:K.7, A:R.13 SO4.13: 7 residues within 4Å: Chain A: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.250, A:H.251 Salt bridges: A:R.53, A:H.249, A:H.251 SO4.14: 6 residues within 4Å: Chain A: W.129, T.164, H.166, K.198, F.256, S.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.164, A:S.257 Salt bridges: A:H.166 SO4.17: 2 residues within 4Å: Chain C: K.7 Chain E: R.13 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Salt bridges: E:R.13, C:K.7 SO4.18: 7 residues within 4Å: Chain C: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.250, C:H.251 Water bridges: C:R.53, C:R.53 Salt bridges: C:R.53, C:H.249 SO4.20: 6 residues within 4Å: Chain E: K.50, R.53, P.151, H.249, A.250, H.251 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.49, E:A.250, E:H.251 Salt bridges: E:R.53, E:H.249, E:H.251 SO4.21: 6 residues within 4Å: Chain E: T.164, H.166, V.238, A.255, F.256, S.257 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.255, E:S.257 Salt bridges: E:H.166 SO4.23: 7 residues within 4Å: Chain G: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Q.248, G:A.250, G:H.251 Salt bridges: G:R.53, G:H.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Llinas, P. et al., Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide. EMBO J. (2005)

Release Date

2005-05-10

Peptides

Urokinase plasminogen activator surface receptor: ACEG
antagonist peptide: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
K

E
M

G
O

B
J

D
L

F
N

H
P

Urokinase plasminogen activator surface receptor

antagonist peptide

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