SMTL ID : 7akk.1

Structure of a complement factor-receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.39 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: T.19, V.21, N.63, L.479, K.480, A.481 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- BMA: beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-BMA.2: 2 residues within 4Å: Chain D: N.63, L.479 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.197, T.198, L.589 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain D: C.537, Q.591 Chain E: V.69 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.537 GOL.9: 9 residues within 4Å: Chain E: I.7, I.8, E.10, I.13, R.115, V.116, E.117, K.165, A.167 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:I.8, E:R.115, E:R.115, E:E.117, E:K.165, E:A.167

2 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: P.208 Chain B: I.51, T.52, D.84 No protein-ligand interaction detected (PLIP) K.7: 3 residues within 4Å: Chain D: P.208, D.577 Chain E: T.52 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain B: D.499 Chain C: D.14, S.16, S.18, T.83, D.116 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:S.16, C:S.18, C:T.83, B:D.499, B:D.499 MG.10: 5 residues within 4Å: Chain F: S.16, G.17, S.18, T.83, E.118 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:S.16, F:S.18, F:T.83

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

NAG.8: 3 residues within 4Å: Chain E: E.186, R.189, N.191 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, F.J. et al., The crystal structure of iC3b-CR3 alpha I reveals a modular recognition of the main opsonin iC3b by the CR3 integrin receptor. Nat Commun (2022)

Release Date

2022-04-13

Peptides

Complement C3 beta chain: AD
Complement C3b alpha' chain: BE
Integrin alpha-M: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
C

B
A

E
E

C
D

F
H

Complement C3 beta chain

Complement C3b alpha' chain

Integrin alpha-M

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