SMTL ID : 8hql.6 (5 other biounits)

Crystal structure of mouse SNX25 PX domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

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

1PE.1: 4 residues within 4Å: Chain A: Q.70, K.89, N.92, Q.93 Ligand excluded by PLIP 1PE.2: 5 residues within 4Å: Chain A: T.11, S.12, F.27, T.44 Ligands: 1PE.11 Ligand excluded by PLIP 1PE.3: 7 residues within 4Å: Chain A: S.9, R.91, N.92, N.95, A.96, Q.99 Ligands: GOL.8 Ligand excluded by PLIP 1PE.4: 3 residues within 4Å: Chain A: S.12 Chain D: R.7, Q.33 Ligand excluded by PLIP 1PE.11: 10 residues within 4Å: Chain A: F.27, N.42, W.43, T.44 Chain B: E.39, T.40, K.41, N.42 Ligands: 1PE.2, 1PE.12 Ligand excluded by PLIP 1PE.12: 9 residues within 4Å: Chain A: E.39, T.40, K.41, N.42 Chain B: R.29, N.42, W.43, T.44 Ligands: 1PE.11 Ligand excluded by PLIP 1PE.13: 9 residues within 4Å: Chain B: S.12, A.13, H.84, G.88, R.91 Chain J: R.7, N.31, Q.33, E.34 Ligand excluded by PLIP 1PE.14: 3 residues within 4Å: Chain B: Q.53, S.73, L.74 Ligand excluded by PLIP 1PE.15: 3 residues within 4Å: Chain B: P.64, S.65, R.106 Ligand excluded by PLIP 1PE.16: 4 residues within 4Å: Chain B: R.7, A.8, S.9, R.29 Ligand excluded by PLIP 1PE.18: 4 residues within 4Å: Chain C: Q.70, K.89, N.92, Q.93 Ligand excluded by PLIP 1PE.19: 5 residues within 4Å: Chain C: T.11, S.12, F.27, T.44 Ligands: 1PE.28 Ligand excluded by PLIP 1PE.20: 7 residues within 4Å: Chain C: S.9, R.91, N.92, N.95, A.96, Q.99 Ligands: GOL.25 Ligand excluded by PLIP 1PE.21: 3 residues within 4Å: Chain B: R.7, Q.33 Chain C: S.12 Ligand excluded by PLIP 1PE.28: 10 residues within 4Å: Chain C: F.27, N.42, W.43, T.44 Chain D: E.39, T.40, K.41, N.42 Ligands: 1PE.19, 1PE.29 Ligand excluded by PLIP 1PE.29: 9 residues within 4Å: Chain C: E.39, T.40, K.41, N.42 Chain D: R.29, N.42, W.43, T.44 Ligands: 1PE.28 Ligand excluded by PLIP 1PE.30: 9 residues within 4Å: Chain D: S.12, A.13, H.84, G.88, R.91 Chain H: R.7, N.31, Q.33, E.34 Ligand excluded by PLIP 1PE.31: 3 residues within 4Å: Chain D: Q.53, S.73, L.74 Ligand excluded by PLIP 1PE.32: 3 residues within 4Å: Chain D: P.64, S.65, R.106 Ligand excluded by PLIP 1PE.33: 4 residues within 4Å: Chain D: R.7, A.8, S.9, R.29 Ligand excluded by PLIP 1PE.35: 7 residues within 4Å: Chain E: W.43, T.44 Chain F: T.40, K.41, N.42 Ligands: CL.40, CL.47 Ligand excluded by PLIP 1PE.36: 2 residues within 4Å: Chain E: E.61, K.67 Ligand excluded by PLIP 1PE.37: 2 residues within 4Å: Chain E: S.65, R.106 Ligand excluded by PLIP 1PE.38: 8 residues within 4Å: Chain E: S.12, A.13, G.88, R.91 Chain I: R.7, N.31, Q.33, E.34 Ligand excluded by PLIP 1PE.42: 7 residues within 4Å: Chain E: T.40, K.41, N.42 Chain F: W.43, T.44 Ligands: CL.40, CL.47 Ligand excluded by PLIP 1PE.43: 2 residues within 4Å: Chain F: E.61, K.67 Ligand excluded by PLIP 1PE.44: 2 residues within 4Å: Chain F: S.65, R.106 Ligand excluded by PLIP 1PE.45: 8 residues within 4Å: Chain F: S.12, A.13, G.88, R.91 Chain G: R.7, N.31, Q.33, E.34 Ligand excluded by PLIP 1PE.49: 9 residues within 4Å: Chain G: R.29, N.42, W.43, T.44 Chain H: E.39, T.40, K.41, N.42 Ligands: CL.55 Ligand excluded by PLIP 1PE.57: 7 residues within 4Å: Chain G: T.40, K.41, N.42 Chain H: R.29, W.43, T.44 Ligands: CL.55 Ligand excluded by PLIP 1PE.58: 2 residues within 4Å: Chain H: S.65, R.106 Ligand excluded by PLIP 1PE.63: 9 residues within 4Å: Chain I: R.29, N.42, W.43, T.44 Chain J: E.39, T.40, K.41, N.42 Ligands: CL.69 Ligand excluded by PLIP 1PE.71: 7 residues within 4Å: Chain I: T.40, K.41, N.42 Chain J: R.29, W.43, T.44 Ligands: CL.69 Ligand excluded by PLIP 1PE.72: 2 residues within 4Å: Chain J: S.65, R.106 Ligand excluded by PLIP

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.59, Q.109, S.110, E.111, A.112 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: Y.114, S.118, P.119 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.47, E.51, A.112, A.115, F.116 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: R.7, A.8, S.9, R.29, N.31 Ligands: 1PE.3 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: P.72, F.86, K.89, Q.93 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain C: L.59, Q.109, S.110, E.111, A.112 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain C: Y.114, S.118, P.119 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: R.47, E.51, A.112, A.115, F.116 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: R.7, A.8, S.9, R.29, N.31 Ligands: 1PE.20 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: P.72, F.86, K.89, Q.93 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain E: Q.53, H.56, Q.70, L.71 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain F: Q.53, H.56, Q.70, L.71 Ligand excluded by PLIP GOL.50: 3 residues within 4Å: Chain G: P.64, S.65, R.106 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain C: E.34 Chain G: S.12, A.13, H.84, G.88 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain G: Q.53, S.73, L.74, S.75 Ligand excluded by PLIP GOL.53: 4 residues within 4Å: Chain G: S.9, R.91, N.95, Q.99 Ligand excluded by PLIP GOL.54: 6 residues within 4Å: Chain G: R.47, E.51, N.54, L.55, A.115, F.116 Ligand excluded by PLIP GOL.59: 3 residues within 4Å: Chain E: R.7 Chain H: H.84 Ligands: GOL.60 Ligand excluded by PLIP GOL.60: 6 residues within 4Å: Chain E: R.7, Q.33, E.34 Chain H: S.12, A.13 Ligands: GOL.59 Ligand excluded by PLIP GOL.61: 5 residues within 4Å: Chain H: M.23, S.50, Q.53, S.73, L.74 Ligand excluded by PLIP GOL.64: 3 residues within 4Å: Chain I: P.64, S.65, R.106 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain A: E.34 Chain I: S.12, A.13, H.84, G.88 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain I: Q.53, S.73, L.74, S.75 Ligand excluded by PLIP GOL.67: 4 residues within 4Å: Chain I: S.9, R.91, N.95, Q.99 Ligand excluded by PLIP GOL.68: 6 residues within 4Å: Chain I: R.47, E.51, N.54, L.55, A.115, F.116 Ligand excluded by PLIP GOL.73: 3 residues within 4Å: Chain F: R.7 Chain J: H.84 Ligands: GOL.74 Ligand excluded by PLIP GOL.74: 6 residues within 4Å: Chain F: R.7, Q.33, E.34 Chain J: S.12, A.13 Ligands: GOL.73 Ligand excluded by PLIP GOL.75: 5 residues within 4Å: Chain J: M.23, S.50, Q.53, S.73, L.74 Ligand excluded by PLIP

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

CL.10: 3 residues within 4Å: Chain A: L.77, K.80, S.81 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: V.38 Chain B: C.25, R.48 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain C: L.77, K.80, S.81 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain C: V.38 Chain D: C.25, R.48 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Ligands: 1PE.35, 1PE.42, CL.47 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Ligands: 1PE.35, CL.40, 1PE.42 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain G: N.42 Ligands: 1PE.49, 1PE.57 Ligand excluded by PLIP CL.62: 5 residues within 4Å: Chain H: S.75, L.77, P.78, F.79, K.80 Ligand excluded by PLIP CL.69: 3 residues within 4Å: Chain I: N.42 Ligands: 1PE.63, 1PE.71 Ligand excluded by PLIP CL.76: 5 residues within 4Å: Chain J: S.75, L.77, P.78, F.79, K.80 Ligand excluded by PLIP

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.41: 3 residues within 4Å: Chain E: Q.53, S.73, L.74 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.53, E:L.74 ACY.48: 3 residues within 4Å: Chain F: Q.53, S.73, L.74 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.53, F:L.74 ACY.56: 2 residues within 4Å: Chain G: S.73, K.80 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.73 Salt bridges: G:K.76, G:K.80 ACY.70: 2 residues within 4Å: Chain I: S.73, K.80 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.73 Salt bridges: I:K.76, I:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Z. et al., Crystal structure of mouse SNX25 PX domain. To Be Published

Release Date

2023-12-20

Peptides

Sorting nexin-25: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
D

F
D

G
C

H
E

I
C

J
E

Sorting nexin-25

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