SMTL ID : 9avs.1

Human alpha-galactosidase A in complex with saposin B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.53 Å

Oligo State

hetero-2-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 8 residues within 4Å: Chain A: V.106, G.107, N.108, F.118, Y.142, C.143, D.144, N.148 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 6 residues within 4Å: Chain A: D.2, N.3, G.4, N.161, G.164, R.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.4, A:D.2 NAG-NAG-BMA-MAN.4: 7 residues within 4Å: Chain B: G.107, N.108, F.118, Y.142, C.143, D.144, N.148 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain A: N.184, T.186, E.187 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.5: 6 residues within 4Å: Chain B: D.2, N.3, G.4, R.7, N.161, G.164 No protein-ligand interaction detected (PLIP)

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

SO4.6: 7 residues within 4Å: Chain A: S.204, W.205, K.206, K.209 Chain B: W.205, K.206, K.209 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.204, A:W.205, A:K.206, B:W.205, B:K.206 Salt bridges: A:K.209, B:K.209 SO4.7: 4 residues within 4Å: Chain A: L.5, A.6, R.7, T.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.6, A:R.7 SO4.8: 5 residues within 4Å: Chain A: R.301, I.336, A.337, S.340, R.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.337, A:S.340 Salt bridges: A:R.301, A:R.371 SO4.9: 3 residues within 4Å: Chain A: L.1, D.2, R.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.189 Salt bridges: A:R.189 SO4.10: 3 residues within 4Å: Chain A: G.303, D.304 Chain C: T.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.304 SO4.11: 4 residues within 4Å: Chain B: R.301, I.336, A.337, R.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.337, B:A.337 Salt bridges: B:R.301, B:R.371 SO4.12: 4 residues within 4Å: Chain B: L.5, A.6, R.7, T.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.6, B:R.7 SO4.13: 2 residues within 4Å: Chain B: T.335, R.371 No protein-ligand interaction detected (PLIP)

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

NAG.14: 3 residues within 4Å: Chain B: N.184, E.187, Q.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.184, B:E.187, B:Q.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sawyer, T.K. et al., Human Saposin B Ligand Binding and Presentation to alpha-Galactosidase A. Biorxiv (2024)

Release Date

2024-04-17

Peptides

Alpha-galactosidase A: AB
Saposin-B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Alpha-galactosidase A

Saposin-B

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