SMTL ID : 4ikb.1

Crystal structure of SNX11 PX domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: C.49, R.51, Q.123 Ligands: PE5.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.123, A:Q.123 SO4.2: 3 residues within 4Å: Chain A: R.53, Y.54, R.55 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.54, A:R.55 Water bridges: A:V.30, A:R.53, A:R.93, A:R.93 Salt bridges: A:R.53 SO4.3: 5 residues within 4Å: Chain A: G.78, K.79, S.80 Chain B: H.99, K.103 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.79, A:S.80 Salt bridges: B:H.99, B:K.103 SO4.4: 3 residues within 4Å: Chain A: W.59, K.62, R.66 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.66, A:R.66, A:E.130 Salt bridges: A:K.62, A:R.66 SO4.5: 1 residues within 4Å: Chain A: R.55 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.53 Salt bridges: A:R.55 SO4.6: 5 residues within 4Å: Chain A: R.61, Q.65, P.72, V.73 Ligands: PE5.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.65, A:V.73, A:V.73 Salt bridges: A:R.61 SO4.13: 3 residues within 4Å: Chain B: R.53, Y.54, R.55 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.55 Water bridges: B:Y.54, B:Y.54, B:K.79, B:K.79, B:R.93 Salt bridges: B:R.53 SO4.14: 1 residues within 4Å: Chain B: K.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63 Salt bridges: B:K.62

5 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.7: 3 residues within 4Å: Chain A: R.61, Q.65 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.61, A:R.61, A:Q.65 PE5.8: 6 residues within 4Å: Chain A: T.81, F.83, G.84, T.85, S.86, F.89 No protein-ligand interaction detected (PLIP) PE5.12: 5 residues within 4Å: Chain A: Q.21, Y.29, D.31, R.51 Ligands: SO4.1 No protein-ligand interaction detected (PLIP) PE5.15: 3 residues within 4Å: Chain B: G.84, T.85, E.88 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.84 PE5.18: 5 residues within 4Å: Chain B: Q.16, D.17, K.33, F.35, C.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.16, B:Q.16, B:K.33

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: G.135, R.136, L.137 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: V.20, Q.21, N.22, E.23 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.10: 1 residues within 4Å: Chain A: K.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.46 NA.16: 2 residues within 4Å: Chain B: D.17, P.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Structure of Sorting Nexin 11 (SNX11) Reveals a Novel Extended PX Domain (PXe Domain) Critical for the Inhibition of Sorting Nexin 10 (SNX10) Induced Vacuolation. to be published

Release Date

2013-04-24

Peptides

Sorting nexin-11: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sorting nexin-11

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