SMTL ID : 6rus.1 (1 other biounit)

Structure of a functional properdin monomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

3 x FUC- BGC: beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose(Post Translational Modification)

FUC-BGC.1: 5 residues within 4Å: Chain A: V.123, T.124, C.125, P.164, H.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.166, A:H.166 FUC-BGC.2: 2 residues within 4Å: Chain A: T.65, C.106 No protein-ligand interaction detected (PLIP) FUC-BGC.3: 7 residues within 4Å: Chain A: A.180, S.181, C.182, P.186, C.227, P.228, N.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230

8 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.4: 3 residues within 4Å: Chain A: L.55, W.56, R.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.56, A:W.56, A:R.73, A:R.73 MAN.5: 2 residues within 4Å: Chain A: T.58, W.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58, A:T.58, A:W.59 MAN.6: 4 residues within 4Å: Chain A: G.111, W.112, R.134, P.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.112, A:W.112, A:R.134, A:R.134 MAN.7: 3 residues within 4Å: Chain A: G.114, W.115, R.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.115, A:W.115, A:R.132, A:R.132 MAN.8: 3 residues within 4Å: Chain A: P.117, W.118, R.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.116, A:W.118, A:R.130 MAN.9: 4 residues within 4Å: Chain A: A.168, W.169, R.195, P.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.169, A:R.195, A:R.195 MAN.10: 3 residues within 4Å: Chain A: T.171, W.172, R.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.170, A:W.172, A:R.193, A:R.193 MAN.11: 3 residues within 4Å: Chain A: G.173, P.174, W.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.173, A:W.175, A:R.219

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

SO4.12: 4 residues within 4Å: Chain A: H.183, R.220, T.222, G.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.223 Salt bridges: A:H.183, A:R.220 SO4.13: 3 residues within 4Å: Chain A: H.183, G.184, R.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.184 Salt bridges: A:H.183, A:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, D.V. et al., Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Front Immunol (2019)

Release Date

2019-08-21

Peptides

Properdin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Properdin

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