SMTL ID : 6rv6.1

Structure of properdin lacking TSR3 based on anomalous data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

hetero-1-1-mer

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, C.163, P.164 No protein-ligand interaction detected (PLIP) FUC-BGC.2: 4 residues within 4Å: Chain A: T.65, C.66, Q.103, P.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.107 Hydrophobic interactions: A:P.107 FUC-BGC.3: 5 residues within 4Å: Chain A: N.32 Chain B: V.17, T.18, C.58, P.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.32

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 3 residues within 4Å: Chain B: E.172, K.173, N.174 No protein-ligand interaction detected (PLIP)

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

MAN.5: 4 residues within 4Å: Chain A: S.54, 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.6: 2 residues within 4Å: Chain A: T.58, W.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58, A:T.58, A:W.59, A:W.59 MAN.7: 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.8: 3 residues within 4Å: Chain A: G.114, W.115, R.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.113, A:W.115, A:R.132 MAN.9: 4 residues within 4Å: Chain A: G.116, P.117, W.118, R.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.118, A:W.118, A:R.130 MAN.10: 4 residues within 4Å: Chain B: D.65, S.66, W.67, R.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.65, B:W.67, B:R.92, B:R.92 MAN.11: 5 residues within 4Å: Chain B: G.68, E.69, W.70, R.114, W.178 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.69, B:W.70, B:W.70, B:R.114, B:W.178 MAN.12: 6 residues within 4Å: Chain B: G.126, S.127, W.128, E.186, E.187, L.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.128, B:W.128, B:E.186 MAN.13: 4 residues within 4Å: Chain B: S.132, T.133, W.134, R.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.132, B:W.134, B:R.147 MAN.14: 3 residues within 4Å: Chain B: E.130, W.131, R.149 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.130, B:E.130, B:W.131, B:W.131, B:R.149, B:R.149 MAN.15: 4 residues within 4Å: Chain B: G.5, W.6, R.28, A.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.6, B:W.6, B:R.28, B:R.28 MAN.16: 3 residues within 4Å: Chain B: G.7, P.8, W.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.7, B:W.9

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
Properdin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Properdin

Properdin

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