SMTL ID : 5m6w.1

Properdin in complex with alternative pathway C3 convertase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.00 Å

Oligo State

hetero-oligomer

Ligands

16 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: T.52, N.63 Ligands: NAG.2 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Ligands: NAG.1, BMA.3, MAN.5 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: E.149, N.178 Chain B: R.187, N.189 Ligands: NAG.8 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: M.179 Ligands: NAG.7, BMA.9, MAN.11 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: T.52, N.63 Ligands: NAG.13 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Ligands: NAG.12, BMA.14, MAN.16 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: N.189 Ligands: NAG.20 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: E.149 Ligands: NAG.19, BMA.21, MAN.23 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain E: S.25, N.26, P.173 Ligands: NAG.26 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Ligands: NAG.25, BMA.27 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: W.118, N.119 Ligands: NAG.29 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Ligands: NAG.28, BMA.30 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain F: S.25, N.26, V.196 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Ligands: NAG.31, BMA.33 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: W.118, N.119 Ligands: NAG.35 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Ligands: NAG.34, BMA.36 Ligand excluded by PLIP

8 x BMA: BETA-D-MANNOSE(Non-functional Binders)

BMA.3: 2 residues within 4Å: Ligands: NAG.2, MAN.4 No protein-ligand interaction detected (PLIP) BMA.9: 2 residues within 4Å: Ligands: NAG.8, MAN.10 No protein-ligand interaction detected (PLIP) BMA.14: 4 residues within 4Å: Ligands: NAG.13, MAN.15, MAN.16, MAN.17 No protein-ligand interaction detected (PLIP) BMA.21: 4 residues within 4Å: Ligands: NAG.20, MAN.22, MAN.23, MAN.24 No protein-ligand interaction detected (PLIP) BMA.27: 1 residues within 4Å: Ligands: NAG.26 No protein-ligand interaction detected (PLIP) BMA.30: 1 residues within 4Å: Ligands: NAG.29 No protein-ligand interaction detected (PLIP) BMA.33: 1 residues within 4Å: Ligands: NAG.32 No protein-ligand interaction detected (PLIP) BMA.36: 1 residues within 4Å: Ligands: NAG.35 No protein-ligand interaction detected (PLIP)

10 x MAN: ALPHA-D-MANNOSE(Non-functional Binders)

MAN.4: 2 residues within 4Å: Ligands: BMA.3, MAN.5 No protein-ligand interaction detected (PLIP) MAN.5: 2 residues within 4Å: Ligands: NAG.2, MAN.4 No protein-ligand interaction detected (PLIP) MAN.10: 2 residues within 4Å: Ligands: BMA.9, MAN.11 No protein-ligand interaction detected (PLIP) MAN.11: 2 residues within 4Å: Ligands: NAG.8, MAN.10 No protein-ligand interaction detected (PLIP) MAN.15: 2 residues within 4Å: Ligands: BMA.14, MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 3 residues within 4Å: Ligands: NAG.13, BMA.14, MAN.15 No protein-ligand interaction detected (PLIP) MAN.17: 1 residues within 4Å: Ligands: BMA.14 No protein-ligand interaction detected (PLIP) MAN.22: 2 residues within 4Å: Ligands: BMA.21, MAN.23 No protein-ligand interaction detected (PLIP) MAN.23: 3 residues within 4Å: Ligands: NAG.20, BMA.21, MAN.22 No protein-ligand interaction detected (PLIP) MAN.24: 1 residues within 4Å: Ligands: BMA.21 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain B: N.913 Chain F: S.19, T.94, D.130, N.134 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Metal complexes: B:N.913, F:S.19, F:T.94 MG.18: 4 residues within 4Å: Chain D: N.913 Chain E: S.19, G.93, T.94 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.19, E:T.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, D.V. et al., Functional and structural insight into properdin control of complement alternative pathway amplification. EMBO J. (2017)

Release Date

2017-03-15

Peptides

Complement C3: AC
Complement C3: BD
Complement factor B: EF
Staphylococcal complement inhibitor: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
G

B
B

D
H

E
J

F
L

G
N

H
Q

Complement C3

Complement C3

Complement factor B

Staphylococcal complement inhibitor

Related Entries With Identical Sequence