SMTL ID : 4pzg.1

Crystal structure of human sorting nexin 10 (SNX10)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

11 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 9 residues within 4Å: Chain A: T.44, M.45, K.46, T.47, R.154 Chain B: M.45, K.46, T.47, R.154 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.46, B:T.47, B:R.154, B:R.154, A:K.46, A:T.47, A:T.47, A:R.154, A:R.154 NO3.2: 3 residues within 4Å: Chain A: N.84, N.87, H.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.84, A:N.87, A:H.90 NO3.3: 5 residues within 4Å: Chain A: I.30, R.53, Y.54, R.55, N.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.53, A:Y.54, A:R.55, A:N.80, A:N.80 NO3.4: 3 residues within 4Å: Chain A: H.27, S.28 Ligands: PE5.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.27, A:H.27 NO3.5: 2 residues within 4Å: Chain A: R.61, Q.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.61, A:R.61, A:Q.65, A:L.73 NO3.11: 4 residues within 4Å: Chain B: Y.54, R.55, N.80 Ligands: NO3.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.55, B:R.55 NO3.12: 6 residues within 4Å: Chain B: Y.54, P.77, S.78, K.79, N.80, R.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.79, B:K.79, B:R.94, B:R.94 NO3.13: 7 residues within 4Å: Chain B: S.28, Y.29, I.30, F.83, M.85, R.94 Ligands: NO3.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.30, B:R.94 NO3.14: 6 residues within 4Å: Chain B: I.30, R.53, Y.54, R.55 Ligands: NO3.11, NO3.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.53, B:Y.54, B:R.55, B:R.55 NO3.15: 3 residues within 4Å: Chain B: N.86, N.87, R.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.88 NO3.16: 2 residues within 4Å: Chain B: H.124, M.152 No protein-ligand interaction detected (PLIP)

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

PE5.6: 7 residues within 4Å: Chain A: T.47, S.48, C.49, N.153, R.154 Chain B: R.154, F.156 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.154, B:F.156 Hydrogen bonds: A:R.154 PE5.7: 2 residues within 4Å: Chain A: R.55, W.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.59 PE5.8: 5 residues within 4Å: Chain A: S.28, N.80, L.81, F.83 Ligands: NO3.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.28 PE5.9: 5 residues within 4Å: Chain A: E.75, L.76, P.77, S.78 Ligands: PE5.10 No protein-ligand interaction detected (PLIP) PE5.10: 4 residues within 4Å: Chain A: R.61, E.75, L.76 Ligands: PE5.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.76 PE5.17: 4 residues within 4Å: Chain B: V.58, R.61, E.75, L.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.61, B:L.76 PE5.18: 7 residues within 4Å: Chain A: F.10, H.37, N.39 Chain B: E.143, E.144, H.147, K.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, T. et al., Structure of human SNX10 reveals insights into its role in human autosomal recessive osteopetrosis. Proteins (2014)

Release Date

2014-09-24

Peptides

Sorting nexin-10: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sorting nexin-10