SMTL ID : 4fww.1

Crystal structure of the Sema-PSI extracellular domains of human RON receptor tyrosine kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.1: 7 residues within 4Å: Chain A: L.401, L.402, V.405, R.429, L.431, Y.444, N.447 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.444

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

SO4.2: 9 residues within 4Å: Chain A: V.228, R.238, R.354, G.356, L.357, D.358, F.359, L.387 Ligands: EDO.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.357, A:D.358, A:D.358 Water bridges: A:V.228 Salt bridges: A:R.238, A:R.354 SO4.3: 4 residues within 4Å: Chain A: C.345, S.380, C.381, R.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.381, A:R.382 Water bridges: A:C.345 Salt bridges: A:R.382

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: E.248, H.383 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.383 ACT.5: 3 residues within 4Å: Chain A: G.352, L.353, R.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.354 Water bridges: A:R.354 ACT.6: 4 residues within 4Å: Chain A: S.438, L.439, N.440, Y.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.439, A:N.440, A:Y.441 ACT.7: 7 residues within 4Å: Chain A: T.52, T.77, T.79, S.93, C.94, G.95, F.103 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.52, A:F.103 Hydrogen bonds: A:S.93 Water bridges: A:T.79 ACT.8: 6 residues within 4Å: Chain A: A.16, M.17, V.81, L.82, R.144, D.460 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.17 Water bridges: A:R.144, A:R.144, A:R.144 Salt bridges: A:R.144

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: L.104, H.105, D.106, A.117, A.118, A.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.104, A:D.106, A:D.106 GOL.10: 4 residues within 4Å: Chain A: F.217, R.241, D.251, D.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.241, A:D.251, A:D.338 Water bridges: A:R.241, A:D.251 GOL.11: 6 residues within 4Å: Chain A: E.248, G.250, D.251, R.382, H.383 Ligands: ACT.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.248, A:D.251, A:H.383 Water bridges: A:L.249 GOL.12: 9 residues within 4Å: Chain A: L.88, Q.152, A.153, S.154, R.179, L.180, K.181, A.182 Ligands: EDO.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.154, A:R.179 Water bridges: A:S.154, A:K.181, A:A.182

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

EDO.13: 5 residues within 4Å: Chain A: R.144, V.209, H.210, S.211, D.460 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.211, A:S.211, A:D.460 Water bridges: A:V.145 EDO.14: 4 residues within 4Å: Chain A: T.19, Y.411, S.462, R.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.19, A:Y.411, A:Y.411, A:R.463 EDO.15: 5 residues within 4Å: Chain A: A.87, E.149, Q.152, S.154 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.149 Water bridges: A:S.154 EDO.16: 7 residues within 4Å: Chain A: A.226, S.227, R.238, V.256, R.354, L.387 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.226, A:R.238, A:R.354

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 6 residues within 4Å: Chain A: A.193, L.249, G.250, H.383, F.384, P.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.383 Water bridges: A:A.193, A:A.193, A:G.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chao, K.L. et al., Crystal Structure of the Sema-PSI Extracellular Domain of Human RON Receptor Tyrosine Kinase. Plos One (2012)

Release Date

2012-08-08

Peptides

Macrophage-stimulating protein receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage-stimulating protein receptor