SMTL ID : 5ybz.1

High resolution structure of complement C1q-like protein 3 C1q domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-trimer

Ligands

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 5 residues within 4Å: Chain A: Q.16, H.17, E.18, R.60 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.16 Salt bridges: A:E.18 DMS.2: 5 residues within 4Å: Chain A: K.14, R.15, Q.16, G.118, N.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.16 DMS.13: 5 residues within 4Å: Chain C: E.18, G.19, Y.20, E.21, V.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.21, C:V.22 Salt bridges: C:E.21 pi-Cation interactions: C:Y.20

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

SO4.3: 4 residues within 4Å: Chain A: K.73, R.78, L.99 Chain C: V.29 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:V.29, A:K.73, A:R.78 Salt bridges: A:K.73, A:R.78 SO4.4: 1 residues within 4Å: Chain A: K.115 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.18, A:E.18, A:E.18, A:K.115 Salt bridges: A:K.115 SO4.5: 6 residues within 4Å: Chain A: Y.92, S.94 Chain B: S.94 Chain C: Y.92, S.94 Ligands: NA.11 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.94, C:S.94, A:S.94, B:S.94 Water bridges: A:Y.92 SO4.8: 4 residues within 4Å: Chain A: V.29 Chain B: K.73, R.78, L.99 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.73, B:R.78 Salt bridges: B:K.73, B:R.78 SO4.9: 3 residues within 4Å: Chain B: D.27, K.123 Chain C: R.78 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.27 Water bridges: B:K.123 Salt bridges: B:K.123, C:R.78 SO4.10: 4 residues within 4Å: Chain B: N.31, L.32, G.33, N.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33 Water bridges: B:N.31 SO4.14: 5 residues within 4Å: Chain B: N.122, Y.124 Chain C: W.68, D.70, S.80 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.80, B:Y.124 SO4.15: 5 residues within 4Å: Chain C: R.15, Q.16, H.117, G.118, G.119 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.16, C:G.118, C:G.119, C:G.119 Water bridges: C:R.15, C:R.15, C:H.117 Salt bridges: C:R.15, C:H.117

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

CL.6: 2 residues within 4Å: Chain A: K.123 Chain B: R.78 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: H.17, E.18, E.21 Ligands: DMS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.18, A:E.21 NA.11: 5 residues within 4Å: Chain B: H.56, Y.92, S.94 Chain C: S.94 Ligands: SO4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.56, B:S.94, C:S.94 Water bridges: B:S.94

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 6 residues within 4Å: Chain A: T.54, S.96 Chain B: T.54, S.96 Chain C: T.54, S.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., High resolution structure of complement C1q-like protein 3 C1q domain. To Be Published

Release Date

2018-10-03

Peptides

Complement C1q-like protein 3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Complement C1q-like protein 3