SMTL ID : 4on3.1

Crystal structure of human sorting nexin 10 (SNX10)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

NO3.1: 5 residues within 4Å: Chain A: I.30, R.53, Y.54, R.55, N.80 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.53, A:R.53, A:Y.54, A:R.55, A:N.80, A:N.80 NO3.2: 3 residues within 4Å: Chain A: N.84, N.87, H.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.84, A:N.87 NO3.3: 4 residues within 4Å: Chain A: K.22, E.23, D.24, F.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.22, A:E.23, A:D.24, A:D.24 NO3.4: 4 residues within 4Å: Chain A: R.19, Q.21, D.31, R.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21, A:Q.21 NO3.5: 4 residues within 4Å: Chain A: H.124, Y.140, A.145, K.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.124 NO3.6: 5 residues within 4Å: Chain A: V.50, R.51, S.123, H.124, F.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.51 NO3.7: 4 residues within 4Å: Chain A: A.68, L.69, L.70, L.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.69, A:L.70, A:V.71 NO3.18: 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 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.46, B:T.47, B:T.47, B:R.154, B:R.154, A:T.44, A:K.46, A:T.47, A:R.154, A:R.154 NO3.19: 6 residues within 4Å: Chain B: I.30, R.53, Y.54, R.55 Ligands: NO3.20, NO3.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.53, B:R.53, B:Y.54, B:R.55 Water bridges: B:R.94 NO3.20: 6 residues within 4Å: Chain B: Y.29, I.30, F.83, M.85, R.94 Ligands: NO3.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.30, B:I.30, B:R.94 NO3.21: 4 residues within 4Å: Chain B: V.50, R.51, H.124, F.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.51 NO3.22: 3 residues within 4Å: Chain B: S.141, V.142, E.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.141, B:V.142, B:E.143 NO3.23: 3 residues within 4Å: Chain B: N.86, N.87, R.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:R.88 NO3.24: 4 residues within 4Å: Chain B: Y.54, R.55, N.80 Ligands: NO3.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.55, B:N.80

10 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 6 residues within 4Å: Chain A: S.28, Y.29, N.80, L.81, F.83 Ligands: 1PE.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.28 1PE.9: 4 residues within 4Å: Chain A: S.78, K.79, F.82 Ligands: 1PE.11 No protein-ligand interaction detected (PLIP) 1PE.10: 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: 3 interactions with chain A Hydrogen bonds: A:T.47, A:C.49, A:N.153 1PE.11: 6 residues within 4Å: Chain A: R.61, E.75, L.76, P.77, S.78 Ligands: 1PE.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.78 1PE.12: 6 residues within 4Å: Chain A: H.27, S.28, Y.29, R.53, R.55 Ligands: 1PE.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.27, A:R.53, A:R.55 1PE.13: 4 residues within 4Å: Chain A: Y.54, K.79, N.80, L.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.81 1PE.25: 12 residues within 4Å: Chain A: F.10, H.37, N.39, M.41, K.46 Chain B: M.41, F.43, T.44, E.143, E.144, H.147, K.148 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.39, B:K.148 1PE.26: 3 residues within 4Å: Chain B: R.61, E.75, L.76 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.75, B:L.76 1PE.27: 3 residues within 4Å: Chain B: R.16, D.17, R.95 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.17 1PE.28: 12 residues within 4Å: Chain A: R.154, F.156 Chain B: M.45, T.47, S.48, C.49, Q.122, I.146, F.149, A.150, N.153, R.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.47, B:T.47, B:C.49, B:N.153

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

NA.14: 1 residues within 4Å: Chain A: R.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.61 NA.15: 5 residues within 4Å: Chain A: I.34, I.36, S.48, C.49, L.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.36, A:S.48 NA.16: 4 residues within 4Å: Chain A: V.11, S.12, V.13, R.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.11, A:V.13 NA.17: 5 residues within 4Å: Chain A: F.43, T.44, H.118, Q.122, I.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.44, A:T.44, A:H.118, A:Q.122 NA.29: 4 residues within 4Å: Chain B: F.43, T.44, H.118, Q.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.44, B:T.44, B:H.118, B:Q.122 NA.30: 5 residues within 4Å: Chain B: I.34, C.35, I.36, S.48, L.121 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.34, B:I.36 NA.31: 1 residues within 4Å: Chain B: Q.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.137 NA.32: 4 residues within 4Å: Chain B: V.11, S.12, V.13, R.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.11, B:V.13, B:R.103

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