SMTL ID : 1ywh.2 (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

3 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.1: 6 residues within 4Å: Chain A: N.52, V.69, S.81, G.82, S.117, E.119 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.69 Hydrogen bonds: A:S.117, A:E.119, A:E.119 NAG-NAG-FUC.3: 6 residues within 4Å: Chain C: T.226, G.227, T.228, N.233, S.235, H.260 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.226 NAG-NAG-FUC.4: 4 residues within 4Å: Chain E: N.52, V.69, S.117, E.119 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.117, E:S.117 Hydrophobic interactions: E:T.27, E:V.29, E:L.40

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

NAG-FUC.2: 4 residues within 4Å: Chain C: N.52, V.69, S.117, E.119 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.117, C:N.52 Water bridges: C:N.52 NAG-FUC.5: 4 residues within 4Å: Chain E: P.154, C.171, N.172, T.173 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.173, E:T.173 NAG-FUC.6: 4 residues within 4Å: Chain G: N.52, T.67, S.117, E.119 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:T.67 Hydrogen bonds: G:N.52, G:N.52, H:D.3, H:Y.8, H:L.9, G:H.251 NAG-FUC.8: 5 residues within 4Å: Chain G: T.226, G.227, T.228, N.233, H.260 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.227 Water bridges: G:H.260

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.7: 1 residues within 4Å: Chain G: N.162 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.162, D.163, F.211 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: P.154, N.172 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain C: I.130, N.162, F.211 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.211 Hydrogen bonds: C:I.130, C:N.162 NAG.15: 2 residues within 4Å: Chain C: P.154, N.172 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.172 NAG.19: 4 residues within 4Å: Chain E: I.130, Q.131, N.162, F.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.131 NAG.23: 2 residues within 4Å: Chain G: P.154, N.172 No protein-ligand interaction detected (PLIP)

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

SO4.11: 2 residues within 4Å: Chain A: K.7 Chain C: R.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.13, A:K.7 SO4.12: 6 residues within 4Å: Chain A: K.50, R.53, P.151, 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:K.50, A:R.53, A:H.251 SO4.13: 2 residues within 4Å: Chain A: R.58, Q.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.58 SO4.16: 6 residues within 4Å: Chain C: E.49, R.53, P.151, H.249, A.250, H.251 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.250, C:H.251 Salt bridges: C:K.50, C:R.53, C:H.249, C:H.251 SO4.17: 2 residues within 4Å: Chain C: R.58, Q.111 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.111 Salt bridges: C:R.58 SO4.18: 5 residues within 4Å: Chain C: T.164, H.166, A.255, F.256, S.257 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.164, C:S.257 Salt bridges: C:H.166 SO4.20: 7 residues within 4Å: Chain E: E.49, K.50, P.151, Q.248, H.249, A.250, H.251 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.250, E:H.251 Salt bridges: E:K.50 SO4.21: 2 residues within 4Å: Chain E: R.58, Q.111 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.111 Salt bridges: E:R.58 SO4.22: 6 residues within 4Å: Chain E: W.129, T.164, H.166, 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 SO4.24: 2 residues within 4Å: Chain E: K.7 Chain G: R.13 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Salt bridges: G:R.13, E:K.7 SO4.25: 6 residues within 4Å: Chain G: K.50, R.53, P.151, H.249, A.250, H.251 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:A.250, G:H.251 Salt bridges: G:K.50, G:R.53, G:H.249, G:H.251 SO4.26: 2 residues within 4Å: Chain G: R.58, Q.111 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.111 Water bridges: G:R.58, G:R.58 Salt bridges: G:R.58 SO4.27: 5 residues within 4Å: Chain G: T.164, H.166, K.198, F.256, S.257 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.257, G:S.257 Salt bridges: G:H.166, G:K.198

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
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Urokinase plasminogen activator surface receptor

antagonist peptide

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