SMTL ID : 5wxu.1

11S globulin from Wrightia tinctoria reveals auxin binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

18 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: H.85, F.93, S.96, N.98, H.168, H.184, R.199 Ligand excluded by PLIP PO4.2: 6 residues within 4Å: Chain A: Y.321, R.413, K.415 Chain F: Y.286, T.289, L.290 Ligand excluded by PLIP PO4.8: 7 residues within 4Å: Chain B: H.85, F.93, S.96, N.98, H.168, H.184, R.199 Ligand excluded by PLIP PO4.9: 6 residues within 4Å: Chain B: Y.321, R.413, K.415 Chain D: Y.286, T.289, L.290 Ligand excluded by PLIP PO4.12: 6 residues within 4Å: Chain B: Y.286, T.289, L.290 Chain D: Y.321, R.413, K.415 Ligand excluded by PLIP PO4.18: 7 residues within 4Å: Chain A: L.290 Chain C: Y.321, R.413, K.415 Chain E: Y.286, T.289, L.290 Ligand excluded by PLIP PO4.19: 7 residues within 4Å: Chain C: H.85, F.93, S.96, N.98, H.168, H.184, R.199 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain C: H.110, A.174, T.175, E.176 Ligand excluded by PLIP PO4.21: 8 residues within 4Å: Chain D: H.85, F.93, S.96, N.98, M.102, H.168, H.184, R.199 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain D: H.110, A.174, T.175, E.176 Ligand excluded by PLIP PO4.24: 4 residues within 4Å: Chain D: N.351, N.411 Chain F: E.190, K.328 Ligand excluded by PLIP PO4.27: 7 residues within 4Å: Chain E: H.85, F.93, S.96, N.98, H.168, H.184, R.199 Ligand excluded by PLIP PO4.28: 6 residues within 4Å: Chain C: Y.286, T.289, L.290 Chain E: Y.321, R.413, K.415 Ligand excluded by PLIP PO4.31: 4 residues within 4Å: Chain D: E.190, K.328 Chain E: N.351, N.411 Ligand excluded by PLIP PO4.33: 4 residues within 4Å: Chain E: H.110, A.174, T.175, E.176 Ligand excluded by PLIP PO4.35: 6 residues within 4Å: Chain A: Y.286, T.289, L.290 Chain F: Y.321, R.413, K.415 Ligand excluded by PLIP PO4.36: 8 residues within 4Å: Chain F: H.85, F.93, S.96, N.98, M.102, H.168, H.184, R.199 Ligand excluded by PLIP PO4.37: 3 residues within 4Å: Chain F: H.110, A.174, T.175 Ligand excluded by PLIP

6 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 7 residues within 4Å: Chain A: K.150, H.152, R.294, I.295, K.296 Chain F: E.303, R.304 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain A Water bridges: F:E.303, A:K.150, A:K.150, A:V.293 Salt bridges: F:R.304, A:K.150, A:H.152, A:H.152, A:K.296, A:K.296 Hydrogen bonds: A:H.152, A:I.295, A:K.296 FLC.11: 8 residues within 4Å: Chain B: K.150, H.152, F.153, R.294, I.295, K.296 Chain D: E.303, R.304 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:K.296 Hydrogen bonds: B:K.150, B:K.150, B:H.152, B:F.153, B:I.295, B:K.296, D:E.303 Salt bridges: B:K.150, B:K.150, B:H.152, B:H.152, B:K.296, D:R.304 Water bridges: D:E.303 FLC.15: 8 residues within 4Å: Chain C: K.150, H.152, F.153, R.294, I.295, K.296 Chain E: E.303, R.304 16 PLIP interactions: 4 interactions with chain E, 12 interactions with chain C Hydrogen bonds: E:E.303, E:E.303, E:E.303, C:F.153, C:I.295, C:K.296 Salt bridges: E:R.304, C:K.150, C:K.150, C:H.152, C:H.152, C:R.294, C:K.296, C:K.296 Hydrophobic interactions: C:H.152 Water bridges: C:K.150 FLC.22: 8 residues within 4Å: Chain B: E.303, R.304 Chain D: K.150, H.152, F.153, R.294, I.295, K.296 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:K.296 Hydrogen bonds: D:F.153, D:I.295, D:K.296, B:E.303 Water bridges: D:K.150, D:K.150, D:K.150 Salt bridges: D:K.150, D:K.150, D:K.150, D:H.152, D:H.152, D:K.296, D:K.296, B:R.304 FLC.30: 8 residues within 4Å: Chain C: E.303, R.304 Chain E: K.150, H.152, F.153, R.294, I.295, K.296 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:K.296 Hydrogen bonds: E:H.152, E:F.153, E:I.295, E:K.296, E:K.296 Salt bridges: E:K.150, E:K.150, E:H.152, E:H.152, E:K.296, C:R.304 Water bridges: C:E.303 FLC.34: 9 residues within 4Å: Chain A: E.303, R.304 Chain F: K.150, H.152, F.153, V.293, R.294, I.295, K.296 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:H.152, F:R.294, F:K.296 Hydrogen bonds: F:V.151, F:F.153, F:I.295, F:K.296, A:E.303 Water bridges: F:H.152, F:V.293 Salt bridges: F:K.150, F:K.150, F:H.152, F:K.296, F:K.296, A:R.304

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: N.50, L.52, S.72, R.73, E.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.50, A:N.50, A:S.72, A:R.73 GOL.5: 4 residues within 4Å: Chain A: R.155, K.296, E.297, N.298 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.155, A:K.296, A:N.298 Water bridges: A:F.153, A:K.296, A:E.297, A:N.298 GOL.6: 3 residues within 4Å: Chain A: A.174, T.175, E.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.175, A:E.176, A:E.176, A:E.176 GOL.10: 5 residues within 4Å: Chain B: R.155, K.296, E.297, N.298, R.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.296, B:N.298, B:R.304 GOL.14: 5 residues within 4Å: Chain B: R.48, N.50, S.72, R.73, E.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.50, B:R.73 GOL.16: 5 residues within 4Å: Chain C: N.50, L.52, S.72, R.73, E.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.50, C:N.50, C:S.72, C:R.73 GOL.17: 6 residues within 4Å: Chain C: D.158, R.294, K.296, E.297, N.298 Ligands: GOL.29 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.294, C:R.294, C:K.296, C:N.298 Water bridges: C:R.294, C:N.298, E:N.298, E:R.304 GOL.29: 6 residues within 4Å: Chain E: R.155, D.158, K.296, E.297, N.298 Ligands: GOL.17 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.155, E:R.155, E:K.296, E:N.298 Water bridges: E:N.298 GOL.39: 4 residues within 4Å: Chain F: N.50, S.72, R.73, E.74 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.50, F:R.73

3 x IAC: 1H-INDOL-3-YLACETIC ACID(Non-covalent)

IAC.7: 10 residues within 4Å: Chain A: G.119, C.120, P.121, E.122 Chain C: R.422 Chain E: G.119, P.121 Chain F: R.422, T.423 Ligands: PEG.38 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: F:T.423, C:R.422 Hydrogen bonds: A:G.119, A:C.120, A:E.122 IAC.13: 12 residues within 4Å: Chain A: R.422, T.423 Chain B: G.119, C.120, P.121 Chain D: R.422, R.427 Chain F: G.119, C.120, P.121, E.122 Ligands: PEG.25 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: A:T.423, D:R.422 Water bridges: A:R.422, D:R.427 Salt bridges: D:R.427 Hydrogen bonds: F:G.119, F:C.120, F:E.122 IAC.26: 12 residues within 4Å: Chain B: R.422, T.423 Chain C: G.119, C.120, P.121 Chain D: G.119, C.120, P.121, E.122 Chain E: R.422, R.427 Ligands: PEG.32 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: E:R.422, B:T.423 Water bridges: E:R.427, D:Q.149 Salt bridges: E:R.427 Hydrogen bonds: D:G.119, D:E.122

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

PEG.25: 7 residues within 4Å: Chain A: R.422, R.427 Chain B: P.121, E.122 Chain D: R.422, R.427 Ligands: IAC.13 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: D:R.422, D:R.427, B:E.122, B:E.122, A:R.422, A:R.427, A:R.427 PEG.32: 7 residues within 4Å: Chain B: R.422, R.427 Chain C: P.121, E.122 Chain E: R.422, R.427 Ligands: IAC.26 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: B:R.422, E:R.422, C:E.122, C:E.122 Water bridges: B:R.422, B:R.427, B:R.427, E:R.427 PEG.38: 6 residues within 4Å: Chain A: P.121, E.122 Chain C: R.422 Chain F: R.422, R.427 Ligands: IAC.7 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F, 2 interactions with chain C Hydrogen bonds: A:E.122, F:R.422, F:R.427, C:R.422, C:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin. Sci Rep (2017)

Release Date

2018-05-23

Peptides

11S globulin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

11S globulin