SMTL ID : 5hgg.1

Crystal structure of uPA in complex with a camelid-derived antibody fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-oligomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: H.171, K.225, D.226, K.227 Chain C: G.10, L.11, Q.122, T.124 Ligands: GOL.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.226, A:K.227, A:K.227, C:T.124 GOL.2: 5 residues within 4Å: Chain A: H.171, Y.172, K.225, D.226 Ligands: GOL.1 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:L.11, A:Q.169 Hydrogen bonds: A:K.225, A:K.225, A:D.226 GOL.3: 5 residues within 4Å: Chain B: H.171, Y.172, K.225, D.226 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.171 Water bridges: B:Q.169 GOL.10: 9 residues within 4Å: Chain B: H.171, K.225, D.226, K.227 Chain D: G.10, L.11, Q.122, T.124 Ligands: GOL.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.171, B:D.226, B:K.227, D:Q.122 GOL.11: 5 residues within 4Å: Chain B: K.225 Chain D: S.7, G.8, G.9, T.121 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.8, D:G.9, D:T.121, D:T.121

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

SO4.4: 4 residues within 4Å: Chain B: S.124, M.125, L.238, R.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.125 Salt bridges: B:R.242 SO4.7: 4 residues within 4Å: Chain C: S.52, S.54, G.56, S.57 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.52, C:S.52, C:S.54, C:G.56

3 x TWN: (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE(Non-covalent)

TWN.5: 11 residues within 4Å: Chain A: T.146 Chain B: T.146 Chain C: R.45, Y.95, W.117 Chain D: Q.39, R.45, Y.95, W.117 Ligands: TWN.6, TWN.9 11 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 6 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.117, C:W.117, A:T.146, D:Q.39, D:Q.39, D:R.45, D:Y.95, D:W.117, B:T.146 Salt bridges: C:R.45, D:R.45 TWN.6: 16 residues within 4Å: Chain A: Y.148 Chain B: Y.148 Chain C: F.37, R.45, G.47, V.48, S.49, Y.60, A.61, H.100, P.101, L.103, E.115, W.117 Chain D: E.44 Ligands: TWN.5 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:F.37, C:E.115, C:W.117, D:E.44, B:Y.148 TWN.9: 18 residues within 4Å: Chain A: Y.148 Chain C: E.44, R.45 Chain D: F.37, R.45, V.48, S.49, C.50, N.59, Y.60, A.61, H.100, P.101, G.102, L.103, E.115, W.117 Ligands: TWN.5 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:Y.148, D:F.37, D:N.59, D:L.103, D:L.103, D:E.115

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 5 residues within 4Å: Chain C: L.11, Q.13, S.126, S.127, A.128 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kromann-Hansen, T. et al., A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior. J.Biol.Chem. (2016)

Release Date

2016-06-01

Peptides

Urokinase-type plasminogen activator: AB
Camelid Derived Antibody Fragment, Nb4: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
S

D
T

Urokinase-type plasminogen activator

Camelid Derived Antibody Fragment, Nb4

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