SMTL ID : 6s08.1

Crystal Structure of Properdin (TSR domains N1 & 456)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

hetero-1-1-mer

Ligands

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

FUC-BGC.1: 5 residues within 4Å: Chain A: V.18, T.19, C.20, P.60 Chain B: N.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.34 Water bridges: B:N.34, B:A.36

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

MAN.2: 5 residues within 4Å: Chain A: G.69, E.70, W.71, R.115, W.179 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.69, A:E.70, A:W.71, A:R.115, A:R.115, A:W.179 Water bridges: A:G.180 MAN.3: 3 residues within 4Å: Chain A: S.67, W.68, R.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.68, A:W.68, A:R.93, A:R.93 MAN.4: 4 residues within 4Å: Chain A: S.128, W.129, E.187, L.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.129, A:W.129, A:E.187 MAN.5: 3 residues within 4Å: Chain A: E.131, W.132, R.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.131, A:W.132, A:W.132, A:R.150, A:R.150 MAN.6: 5 residues within 4Å: Chain A: G.6, W.7, R.29, C.43, A.44 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.7, A:W.7, A:R.29, A:R.29 MAN.7: 3 residues within 4Å: Chain A: P.9, W.10, R.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.10, A:W.10, A:R.49, A:R.49 MAN.9: 4 residues within 4Å: Chain A: S.133, T.134, W.135, R.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.135, A:W.135, A:R.148 MAN.11: 4 residues within 4Å: Chain B: S.56, L.57, W.58, R.75 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.56, B:W.58, B:R.75, B:R.75

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 7 residues within 4Å: Chain A: S.72, P.73, I.75, R.77, Q.90, Q.91, S.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.72, A:R.77 Water bridges: A:Q.90

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

NA.10: 5 residues within 4Å: Chain A: I.82, Q.85, I.87, Y.118, S.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.85, A:I.87, A:S.119 Water bridges: A:C.84

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.12: 2 residues within 4Å: Chain B: T.67, C.68 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van den Bos, R.M. et al., Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b. Front Immunol (2019)

Release Date

2019-09-04

Peptides

Properdin: A
Properdin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Properdin

Properdin

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