SMTL ID : 3poi.3 (5 other biounits)

Crystal structure of MASP-1 CUB2 domain bound to Methylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:D.101, A:S.103, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain B: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.54, B:D.101, B:S.103, H2O.5, H2O.5 CA.9: 4 residues within 4Å: Chain C: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.54, C:D.101, C:S.103, H2O.10, H2O.10 CA.13: 4 residues within 4Å: Chain D: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.54, D:D.64, D:S.103, H2O.15, H2O.15 CA.15: 4 residues within 4Å: Chain E: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.54, E:D.64, E:S.103, H2O.19, H2O.19 CA.17: 4 residues within 4Å: Chain F: E.54, D.64, D.101, S.103 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.54, F:D.64, F:S.103, H2O.23, H2O.23

3 x NME: METHYLAMINE(Non-covalent)

NME.2: 4 residues within 4Å: Chain A: E.54, Y.63, D.101, S.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.101 NME.6: 4 residues within 4Å: Chain B: E.54, Y.63, D.101, S.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.54 NME.10: 4 residues within 4Å: Chain C: E.54, Y.63, D.101, S.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.54

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

SO4.3: 5 residues within 4Å: Chain A: R.107 Chain B: R.107 Chain C: R.107 Ligands: SO4.7, SO4.11 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Salt bridges: C:R.107, A:R.107, B:R.107 Water bridges: B:R.107 SO4.7: 5 residues within 4Å: Chain A: R.107 Chain B: R.107 Chain C: R.107 Ligands: SO4.3, SO4.11 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Water bridges: C:R.107 Salt bridges: C:R.107, A:R.107, B:R.107 SO4.11: 5 residues within 4Å: Chain A: R.107 Chain B: R.107 Chain C: R.107 Ligands: SO4.3, SO4.7 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Salt bridges: C:R.107, A:R.107, B:R.107 Water bridges: A:R.107 SO4.14: 5 residues within 4Å: Chain D: R.107 Chain E: R.107 Chain F: R.107 Ligands: SO4.16, SO4.18 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D Salt bridges: F:R.107, E:R.107, D:R.107 SO4.16: 5 residues within 4Å: Chain D: R.107 Chain E: R.107 Chain F: R.107 Ligands: SO4.14, SO4.18 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E Salt bridges: D:R.107, F:R.107, E:R.107 SO4.18: 5 residues within 4Å: Chain D: R.107 Chain E: R.107 Chain F: R.107 Ligands: SO4.14, SO4.16 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E Salt bridges: D:R.107, F:R.107, E:R.107

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 10 residues within 4Å: Chain A: F.47, E.48, D.49, S.83 Chain C: D.20, Y.21, P.22, N.23 Chain D: T.13, R.114 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:D.20, C:Y.21, C:N.23, A:E.48, A:S.83 Water bridges: C:D.20, A:D.49, A:S.83 TRS.8: 10 residues within 4Å: Chain A: D.20, Y.21, P.22, N.23 Chain B: F.47, E.48, D.49, S.83 Chain E: T.13, R.114 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.20, A:Y.21, A:N.23, B:E.48, B:S.83 Water bridges: A:D.20, B:D.49, B:S.83 TRS.12: 10 residues within 4Å: Chain B: D.20, Y.21, P.22, N.23 Chain C: F.47, E.48, D.49, S.83 Chain F: T.13, R.114 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.20, B:Y.21, B:N.23, C:E.48, C:S.83 Water bridges: B:D.20, C:D.49, C:S.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gingras, A.R. et al., Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation. Structure (2011)

Release Date

2011-08-24

Peptides

Mannan-binding lectin serine protease 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Mannan-binding lectin serine protease 1

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