SMTL ID : 4wrf.1

Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D) Complexed with Mannose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.115, N.117, E.122, N.134, D.135 Ligands: MAN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.115, A:E.122, A:D.135, A:D.135 CA.2: 5 residues within 4Å: Chain A: D.91, E.95, G.120, E.122, D.123 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.91, A:E.95, A:E.122, H2O.5, H2O.5 CA.3: 2 residues within 4Å: Chain A: G.120, D.123 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.120, A:D.123, A:D.123, H2O.1 CA.7: 6 residues within 4Å: Chain B: E.115, N.117, E.122, N.134, D.135 Ligands: MAN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.115, B:E.122, B:D.135, B:D.135 CA.8: 5 residues within 4Å: Chain B: D.91, E.95, G.120, E.122, D.123 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.91, B:E.95, B:E.122, H2O.9, H2O.9 CA.9: 2 residues within 4Å: Chain B: G.120, D.123 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.120, B:D.123, B:D.123, H2O.5 CA.13: 6 residues within 4Å: Chain C: E.115, N.117, E.122, N.134, D.135 Ligands: MAN.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.115, C:E.122, C:D.135, C:D.135 CA.14: 5 residues within 4Å: Chain C: D.91, E.95, G.120, E.122, D.123 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.91, C:E.95, C:E.122, H2O.13, H2O.13 CA.15: 2 residues within 4Å: Chain C: G.120, D.123 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:G.120, C:D.123, C:D.123, H2O.10

3 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.4: 7 residues within 4Å: Chain A: E.115, N.117, E.122, N.134, D.135, R.136 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.117, A:E.122, A:N.134, A:N.134, A:R.136 MAN.10: 7 residues within 4Å: Chain B: E.115, N.117, E.122, N.134, D.135, R.136 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.117, B:E.122, B:N.134, B:N.134, B:R.136 MAN.16: 7 residues within 4Å: Chain C: E.115, N.117, E.122, N.134, D.135, R.136 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.117, C:E.122, C:N.134, C:N.134, C:R.136

3 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.5: 9 residues within 4Å: Chain A: G.29, S.30, M.31, L.32, S.40, T.41, S.76, I.77, K.80 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.32, A:L.32, A:K.80 Hydrogen bonds: A:S.40, A:T.41 Water bridges: B:Q.28 HEZ.11: 9 residues within 4Å: Chain B: G.29, S.30, M.31, L.32, S.40, T.41, S.76, I.77, K.80 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.32, B:L.32, B:K.80 Hydrogen bonds: B:S.40, B:T.41 Water bridges: C:Q.28 HEZ.17: 9 residues within 4Å: Chain C: G.29, S.30, M.31, L.32, S.40, T.41, S.76, I.77, K.80 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.32, C:L.32, C:K.80 Hydrogen bonds: C:S.40, C:T.41 Water bridges: A:Q.28

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: G.137, C.138, L.139, Q.140 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: G.137, C.138, L.139, Q.140 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: G.137, C.138, L.139, Q.140 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Rynkiewicz, M.J. et al., Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop. To be published

Release Date

2016-02-10

Peptides

Pulmonary surfactant-associated protein A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Pulmonary surfactant-associated protein A

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