SMTL ID : 4nn0.1 (2 other biounits)

Crystal structure of the C1QTNF5 globular domain in space group P63

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-trimer

Ligands

36 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 10 residues within 4Å: Chain A: H.55, A.56, S.89, L.90, S.91 Chain B: F.77, L.90, S.91 Ligands: EDO.15, EDO.29 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: P.87, K.121, T.122 Chain B: F.78 Ligands: EDO.5, EDO.9 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: K.86 Ligands: EDO.5 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: P.17, D.19 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain B: Y.113 Ligands: EDO.2, EDO.3 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: T.39, K.41, Q.103 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: A.1, W.135 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: A.1, R.2 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Y.59, P.85, K.86, P.87, Y.117 Ligands: EDO.2 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: K.8, R.26, V.27, L.28 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.133, D.134, W.135 Chain C: R.2 Ligands: EDO.7 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain A: R.60 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain B: H.55, A.56, S.89, L.90, S.91 Chain C: F.77, L.90, S.91 Ligands: EDO.1, EDO.29 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: P.87, K.121, T.122 Chain C: F.78 Ligands: EDO.19, EDO.23 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain B: K.86 Ligands: EDO.19 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: P.17, D.19 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain C: Y.113 Ligands: EDO.16, EDO.17 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: T.39, K.41, Q.103 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: A.1, W.135 Ligands: EDO.25 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: A.1, R.2 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: Y.59, P.85, K.86, P.87, Y.117 Ligands: EDO.16 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: K.8, R.26, V.27, L.28 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: R.2 Chain B: S.133, D.134, W.135 Ligands: EDO.21 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain B: R.60 Ligand excluded by PLIP EDO.29: 10 residues within 4Å: Chain A: F.77, L.90, S.91 Chain C: H.55, A.56, S.89, L.90, S.91 Ligands: EDO.1, EDO.15 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: F.78 Chain C: P.87, K.121, T.122 Ligands: EDO.33, EDO.37 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain C: K.86 Ligands: EDO.33 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain C: P.17, D.19 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: Y.113 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: T.39, K.41, Q.103 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: A.1, W.135 Ligands: EDO.39 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain C: A.1, R.2 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain C: Y.59, P.85, K.86, P.87, Y.117 Ligands: EDO.30 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: K.8, R.26, V.27, L.28 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: R.2 Chain C: S.133, D.134, W.135 Ligands: EDO.35 Ligand excluded by PLIP EDO.40: 1 residues within 4Å: Chain C: R.60 Ligand excluded by PLIP

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.27, SO4.41 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Water bridges: C:G.82, C:W.84, B:W.84, A:W.84 SO4.27: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.13, SO4.41 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Water bridges: B:W.84, A:G.82, A:W.84, C:W.84 SO4.41: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.13, SO4.27 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Water bridges: B:G.82, B:W.84, A:W.84, C:W.84

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 3 residues within 4Å: Chain A: S.12, R.60, Y.117 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.117 Hydrogen bonds: A:R.13, A:Y.117 Water bridges: A:S.12, A:R.13 Salt bridges: A:R.60 ACT.28: 3 residues within 4Å: Chain B: S.12, R.60, Y.117 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.117 Hydrogen bonds: B:R.13, B:Y.117 Water bridges: B:S.12, B:R.13 Salt bridges: B:R.60 ACT.42: 3 residues within 4Å: Chain C: S.12, R.60, Y.117 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.117 Hydrogen bonds: C:R.13, C:Y.117 Water bridges: C:S.12, C:R.13 Salt bridges: C:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, X. et al., The macular degeneration-linked C1QTNF5 (S163) mutation causes higher-order structural rearrangements. J.Struct.Biol. (2014)

Release Date

2014-03-26

Peptides

Complement C1q tumor necrosis factor-related protein 5: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Complement C1q tumor necrosis factor-related protein 5

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