SMTL ID : 4nn0.2 (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

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

EDO.1: 4 residues within 4Å: Chain A: F.78 Chain B: P.87, K.121, T.122 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: A.1, R.2, Q.32, H.34, V.46 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.2 EDO.3: 10 residues within 4Å: Chain A: F.77, L.90, S.91 Chain B: H.55, A.56, S.89, L.90, S.91 Ligands: EDO.11, EDO.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.56, A:S.91 EDO.4: 6 residues within 4Å: Chain A: P.16, P.17, A.20, P.21, L.22, P.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.17 Water bridges: A:P.21 EDO.5: 2 residues within 4Å: Chain A: K.41, Q.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.41, A:Q.103 Water bridges: A:T.39, A:T.43 EDO.9: 4 residues within 4Å: Chain B: F.78 Chain C: P.87, K.121, T.122 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: A.1, R.2, Q.32, H.34, V.46 Ligands: SO4.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.2 EDO.11: 10 residues within 4Å: Chain B: F.77, L.90, S.91 Chain C: H.55, A.56, S.89, L.90, S.91 Ligands: EDO.3, EDO.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.91, C:A.56 EDO.12: 6 residues within 4Å: Chain B: P.16, P.17, A.20, P.21, L.22, P.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.17 Water bridges: B:P.21 EDO.13: 2 residues within 4Å: Chain B: K.41, Q.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.41, B:Q.103 Water bridges: B:T.39, B:T.43 EDO.17: 4 residues within 4Å: Chain A: P.87, K.121, T.122 Chain C: F.78 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain C: A.1, R.2, Q.32, H.34, V.46 Ligands: SO4.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.2 EDO.19: 10 residues within 4Å: Chain A: H.55, A.56, S.89, L.90, S.91 Chain C: F.77, L.90, S.91 Ligands: EDO.3, EDO.11 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.91, A:A.56 EDO.20: 6 residues within 4Å: Chain C: P.16, P.17, A.20, P.21, L.22, P.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.17 Water bridges: C:P.21 EDO.21: 2 residues within 4Å: Chain C: K.41, Q.103 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.41, C:Q.103 Water bridges: C:T.39, C:T.43

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

SO4.6: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.14, SO4.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.84 SO4.7: 3 residues within 4Å: Chain A: A.1, R.2 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.2 SO4.14: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.6, SO4.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.84 SO4.15: 3 residues within 4Å: Chain B: A.1, R.2 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.2 SO4.22: 5 residues within 4Å: Chain A: W.84 Chain B: W.84 Chain C: W.84 Ligands: SO4.6, SO4.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.84 SO4.23: 3 residues within 4Å: Chain C: A.1, R.2 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.2

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

ACT.8: 4 residues within 4Å: Chain A: S.12, R.13, R.60, Y.117 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.117 Hydrogen bonds: A:R.13, A:Y.117 Salt bridges: A:R.60 ACT.16: 4 residues within 4Å: Chain B: S.12, R.13, R.60, Y.117 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.117 Hydrogen bonds: B:R.13, B:Y.117 Salt bridges: B:R.60 ACT.24: 4 residues within 4Å: Chain C: S.12, R.13, R.60, Y.117 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.117 Hydrogen bonds: C:R.13, C:Y.117 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
B

B
B

C
B

Complement C1q tumor necrosis factor-related protein 5

Related Entries With Identical Sequence