SMTL ID : 4d7y.1

Crystal structure of mouse C1QL1 globular domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-trimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CL.5, CD.8, CL.12, CD.15, CL.19 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.89, A:D.89, C:D.89, C:D.89, B:D.89 CD.2: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: CD.9, CD.16 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.93, C:D.93, B:D.93, H2O.3, H2O.10 CD.8: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CD.1, CL.5, CL.12, CD.15, CL.19 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Metal complexes: A:D.89, A:D.89, C:D.89, B:D.89, B:D.89 CD.9: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: CD.2, CD.16 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.93, C:D.93, B:D.93, H2O.3, H2O.10 CD.15: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CD.1, CL.5, CD.8, CL.12, CL.19 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Metal complexes: A:D.89, C:D.89, C:D.89, B:D.89, B:D.89 CD.16: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: CD.2, CD.9 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.93, A:D.93, C:D.93, H2O.3, H2O.10

6 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: NI.10, NI.17 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.93, C:D.93, B:D.93, H2O.3, H2O.6, H2O.9 NI.4: 5 residues within 4Å: Chain A: D.87 Chain B: D.87 Chain C: D.87 Ligands: NI.11, NI.18 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.87, A:D.87, B:D.87, H2O.3, H2O.6, H2O.9 NI.10: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: NI.3, NI.17 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.93, C:D.93, B:D.93, H2O.3, H2O.6, H2O.9 NI.11: 5 residues within 4Å: Chain A: D.87 Chain B: D.87 Chain C: D.87 Ligands: NI.4, NI.18 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.87, A:D.87, B:D.87, H2O.3, H2O.6, H2O.9 NI.17: 5 residues within 4Å: Chain A: D.93 Chain B: D.93 Chain C: D.93 Ligands: NI.3, NI.10 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.93, A:D.93, C:D.93, H2O.3, H2O.6, H2O.9 NI.18: 5 residues within 4Å: Chain A: D.87 Chain B: D.87 Chain C: D.87 Ligands: NI.4, NI.11 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.87, A:D.87, B:D.87, H2O.3, H2O.6, H2O.9

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

CL.5: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CD.1, CD.8, CL.12, CD.15, CL.19 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Ligands: CL.14, CL.21 Ligand excluded by PLIP CL.12: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CD.1, CL.5, CD.8, CD.15, CL.19 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Ligands: CL.7, CL.21 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain A: D.89 Chain B: D.89 Chain C: D.89 Ligands: CD.1, CL.5, CD.8, CL.12, CD.15 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Ligands: CL.7, CL.14 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.72, D.114 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.72, A:D.114, H2O.2, H2O.2, H2O.2 MG.13: 2 residues within 4Å: Chain B: D.72, D.114 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.72, B:D.114, H2O.6, H2O.6, H2O.6 MG.20: 2 residues within 4Å: Chain C: D.72, D.114 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.72, C:D.114, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakegawa, W. et al., Anterograde C1Ql1 Signaling is Required in Order to Determine and Maintain a Single-Winner Climbing Fiber in the Mouse Cerebellum. Neuron (2015)

Release Date

2015-01-28

Peptides

C1Q-RELATED FACTOR: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

C1Q-RELATED FACTOR