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

crystal structure of urokinase plasminogen activator receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-8-8-mer

Ligands

4 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 NAG-NAG-FUC.12: 4 residues within 4Å: Chain K: N.52, S.117, P.118, E.119 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.119

8 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 NAG-FUC.9: 6 residues within 4Å: Chain I: N.52, V.69, R.83, V.85, S.117, E.119 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.83, I:V.85, I:S.117, I:S.117, I:N.52 NAG-FUC.11: 5 residues within 4Å: Chain I: T.226, G.227, T.228, N.233, H.260 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:T.226 Hydrogen bonds: I:N.233 NAG-FUC.14: 4 residues within 4Å: Chain M: N.52, V.69, S.117, E.119 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:S.117, M:S.117, M:N.52 NAG-FUC.17: 4 residues within 4Å: Chain O: N.52, V.69, S.117, E.119 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:S.117, O:S.117

2 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) NAG-NAG.16: 2 residues within 4Å: Chain M: P.154, N.172 No protein-ligand interaction detected (PLIP)

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.10: 3 residues within 4Å: Chain I: I.130, N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 2 residues within 4Å: Chain K: N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 2 residues within 4Å: Chain M: N.162, F.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 3 residues within 4Å: Chain O: I.130, N.162, F.211 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: N.162, D.163, F.211 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain A: P.154, N.172 No protein-ligand interaction detected (PLIP) NAG.24: 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.25: 2 residues within 4Å: Chain C: P.154, N.172 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.172 NAG.29: 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.33: 2 residues within 4Å: Chain G: P.154, N.172 No protein-ligand interaction detected (PLIP) NAG.38: 1 residues within 4Å: Chain I: N.172 No protein-ligand interaction detected (PLIP) NAG.42: 1 residues within 4Å: Chain K: N.172 No protein-ligand interaction detected (PLIP) NAG.43: 2 residues within 4Å: Chain K: N.233, H.260 No protein-ligand interaction detected (PLIP) NAG.46: 3 residues within 4Å: Chain M: T.228, N.233, H.260 No protein-ligand interaction detected (PLIP) NAG.49: 1 residues within 4Å: Chain O: N.172 No protein-ligand interaction detected (PLIP)

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

SO4.21: 2 residues within 4Å: Chain A: K.7 Chain C: R.13 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain A: K.50, R.53, P.151, H.249, A.250, H.251 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: R.58, Q.111 Chain I: R.58, Q.111 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain C: E.49, R.53, P.151, H.249, A.250, H.251 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: R.58, Q.111 Chain O: R.58, Q.111 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain C: T.164, H.166, A.255, F.256, S.257 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain E: E.49, K.50, P.151, Q.248, H.249, A.250, H.251 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: R.58, Q.111 Chain M: R.58, Q.111 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain E: W.129, T.164, H.166, A.255, F.256, S.257 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain E: K.7 Chain G: R.13 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain G: K.50, R.53, P.151, H.249, A.250, H.251 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain G: R.58, Q.111 Chain K: R.58, Q.111 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain G: T.164, H.166, K.198, F.256, S.257 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain I: R.13 Chain O: K.7 Ligand excluded by PLIP SO4.40: 7 residues within 4Å: Chain I: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain I: W.129, T.164, H.166, K.198, F.256, S.257 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain K: K.7 Chain M: R.13 Ligand excluded by PLIP SO4.45: 7 residues within 4Å: Chain K: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 Ligand excluded by PLIP SO4.47: 6 residues within 4Å: Chain M: K.50, R.53, P.151, H.249, A.250, H.251 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain M: T.164, H.166, V.238, A.255, F.256, S.257 Ligand excluded by PLIP SO4.50: 7 residues within 4Å: Chain O: E.49, R.53, P.151, Q.248, H.249, A.250, H.251 Ligand excluded by PLIP

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: ACEGIKMO
antagonist peptide: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

Urokinase plasminogen activator surface receptor

antagonist peptide

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