SMTL ID : 4d9q.3 (2 other biounits)

Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-2-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.116, V.117, V.148, L.149, D.150, R.151, M.169, C.170 Chain C: Y.54 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:V.117, A:R.151, A:C.170, C:Y.54 GOL.2: 7 residues within 4Å: Chain A: L.122, D.124, L.145, V.188, C.189, G.190, G.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.122, A:G.190, A:G.191 GOL.3: 4 residues within 4Å: Chain A: Q.111, R.115, D.116, E.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.111 Water bridges: A:Q.111, A:R.115 GOL.6: 6 residues within 4Å: Chain A: R.157, T.158, H.159, K.209 Chain B: D.31, D.32 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.209, B:D.31 Water bridges: A:D.161, A:K.209, B:D.31, B:D.32 GOL.7: 6 residues within 4Å: Chain B: L.54, R.55, P.56, G.57, V.58, S.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.54, B:G.57, B:S.60 GOL.10: 4 residues within 4Å: Chain C: K.19, S.71, L.72, Y.80 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.19, C:K.19, C:S.71, C:S.71 GOL.11: 6 residues within 4Å: Chain C: R.38, E.46, D.63, F.64, R.67, F.68 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.38, C:D.63, C:D.63, C:R.67 GOL.12: 9 residues within 4Å: Chain D: D.116, V.117, V.148, L.149, D.150, R.151, M.169, C.170 Chain E: Y.54 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:V.117, D:V.117, D:R.151, D:C.170, E:Y.54 Water bridges: D:D.116 GOL.13: 7 residues within 4Å: Chain D: N.206, K.208, K.209 Chain F: D.30, D.31, D.32 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.206, D:K.209, D:K.209 GOL.17: 7 residues within 4Å: Chain E: P.9, V.93, Q.107, G.108, T.109, L.110, P.151 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.110 Water bridges: E:Y.95, E:Q.107, E:Q.107

7 x ZN: ZINC ION(Non-covalent)

ZN.4: 1 residues within 4Å: Chain A: E.118 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.118, A:E.118 ZN.8: 2 residues within 4Å: Chain B: D.1 Chain D: H.133 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.133, B:D.1, H2O.13 ZN.9: 2 residues within 4Å: Chain B: N.138 Chain C: H.166 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.166 ZN.14: 2 residues within 4Å: Chain D: H.41, D.45 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.41, D:D.45 ZN.18: 2 residues within 4Å: Chain E: H.166 Chain F: N.138 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.166 ZN.19: 2 residues within 4Å: Chain B: D.30 Chain F: D.28 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.28, H2O.7 ZN.20: 3 residues within 4Å: Chain F: D.31, D.32 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.32

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

SO4.5: 4 residues within 4Å: Chain A: R.136, P.138, D.139, R.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.139, A:R.140 Salt bridges: A:R.136, A:R.140 SO4.15: 4 residues within 4Å: Chain D: R.136, P.138, D.139, R.140 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.139, D:R.140 Water bridges: D:E.6, D:Q.142 Salt bridges: D:R.136, D:R.140 SO4.16: 7 residues within 4Å: Chain D: S.178, C.179, K.180, S.183, T.198, G.200, R.202 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:C.179 Water bridges: D:K.180, D:R.202 Salt bridges: D:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katschke, K.J. et al., Inhibiting alternative pathway complement activation by targeting the factor d exosite. J.Biol.Chem. (2012)

Release Date

2012-02-22

Peptides

Factor D: AD
Anti-Factor D, light chain: BF
Anti-Factor D, heavy chain: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
D

F
L

C
E

E
H

Factor D

Anti-Factor D, light chain

Anti-Factor D, heavy chain

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