SMTL ID : 3hrz.1

Cobra Venom Factor (CVF) in complex with human factor B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain D: S.93, Y.95, N.97, D.100 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: E.142, K.180, P.185, N.187 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.189 NAG.7: 4 residues within 4Å: Chain C: N.83, S.85, K.103, C.105 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.83 NAG.10: 2 residues within 4Å: Chain D: E.101, N.117 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: P.494, D.517, V.518, D.520 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.494, A:D.517, A:V.518, A:D.520, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain C: T.379 Chain D: S.253, S.255, T.328 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:T.379, D:S.253, D:S.255, D:T.328, H2O.20, H2O.21

1 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: F.240, S.295, V.296, T.297 Chain C: Y.198 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Metal complexes: A:F.240, A:S.295, A:S.295, A:T.297, C:Y.198

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 7 residues within 4Å: Chain A: I.149, V.151, S.171 Chain B: I.232, Q.234 Chain C: L.63, F.65 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.39 P6G.8: 8 residues within 4Å: Chain A: G.303, S.304, D.305, M.306 Chain C: Y.196, L.201, E.203, K.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.306

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 2 residues within 4Å: Chain B: K.197 Chain C: K.57 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:K.57 Salt bridges: C:K.57, B:K.197 PO4.9: 4 residues within 4Å: Chain C: K.264, D.317, H.349, E.350 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.350 Water bridges: C:K.262, C:K.262, C:K.262, C:D.317 Salt bridges: C:K.264, C:H.349 PO4.12: 4 residues within 4Å: Chain B: R.178 Chain D: R.80, H.82, S.167 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.167 Water bridges: D:H.82, D:S.167, B:R.178 Salt bridges: D:R.80, D:H.82, B:R.178 PO4.13: 2 residues within 4Å: Chain D: K.604, H.681 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.681 Water bridges: D:H.681, D:H.681 Salt bridges: D:K.604, D:H.681 PO4.14: 7 residues within 4Å: Chain D: S.212, L.213, R.356, D.396, D.399, K.421, E.424 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.396, D:D.399 Water bridges: D:E.215, D:E.215, D:R.356, D:K.421, D:K.421, D:K.421, D:K.421 Salt bridges: D:R.356, D:K.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssen, B.J. et al., Insights into complement convertase formation based on the structure of the factor B-cobra venom factor complex. Embo J. (2009)

Release Date

2009-07-07

Peptides

Cobra venom factor: A
Cobra venom factor: B
Cobra venom factor: C
Complement factor B: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cobra venom factor

Cobra venom factor

Cobra venom factor

Complement factor B

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