SMTL ID : 7ad7.1

Crystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-1-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: 2 residues within 4Å: Chain B: S.860, N.911 No protein-ligand interaction detected (PLIP)

4 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 2 residues within 4Å: Chain A: Y.121, D.208 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.121 EOH.3: 4 residues within 4Å: Chain A: L.382, G.384, V.413, D.414 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.382 Hydrogen bonds: A:L.382, A:G.384 EOH.5: 3 residues within 4Å: Chain A: W.599 Chain B: S.805, N.806 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.599 EOH.9: 2 residues within 4Å: Chain C: Y.11, W.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.26

1 x MHA: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID(Non-covalent)

MHA.4: 5 residues within 4Å: Chain A: Q.80, Y.501, H.511, F.512, G.513 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.80, A:F.512 Water bridges: A:Y.501, A:R.515, A:R.515 Salt bridges: A:H.511

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain B: H.1002, D.1425, Y.1496, P.1501 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.1002, B:P.1501 Hydrogen bonds: B:H.1002 Water bridges: B:D.1425 MPD.7: 6 residues within 4Å: Chain B: K.1046, N.1090, K.1091, Y.1092, V.1093, E.1094 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.1094 Hydrogen bonds: B:K.1046, B:K.1046

1 x CYS: CYSTEINE(Non-covalent)

CYS.8: 2 residues within 4Å: Chain B: Y.700, C.704 No protein-ligand interaction detected (PLIP)

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.10: 2 residues within 4Å: Chain C: W.9, W.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.26, C:W.26 Hydrogen bonds: C:W.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Macpherson, A. et al., The allosteric modulation of Complement C5 by knob domain peptides. Elife (2021)

Release Date

2021-03-10

Peptides

Complement C5: AB
K8 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Complement C5

K8 peptide

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