SMTL ID : 1ym0.2 (1 other biounit)

Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG-MAN-MAN-FUC-FUC.1: 13 residues within 4Å: Chain A: Y.121, R.122, K.123, N.149, F.155, N.175 Chain B: L.24, P.26, G.27 Chain C: D.196, S.198 Chain D: Q.10 Ligands: SO4.5 7 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: A:F.155, A:Y.121, A:V.120, A:T.152 Water bridges: A:G.177, D:Q.1, D:Q.1, A:N.153 Hydrogen bonds: B:G.27, C:D.114 NAG-NAG-MAN-MAN-FUC-FUC.7: 13 residues within 4Å: Chain A: D.196, S.198 Chain B: Q.10 Chain C: Y.121, R.122, K.123, N.149, F.155, N.175 Chain D: L.24, P.26, G.27 Ligands: SO4.11 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.27 Hydrophobic interactions: C:F.155, C:Y.121 Water bridges: C:G.177

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.157, Y.160, D.163, T.164 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.157, A:D.157, A:Y.160, A:D.163 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: D.157, Y.160, D.163, T.164 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.157, C:D.157, C:Y.160, C:D.163 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.5: 3 residues within 4Å: Chain A: R.122, K.123 Ligands: NAG-NAG-MAN-MAN-FUC-FUC.1 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:G.197 Hydrogen bonds: A:K.123 Salt bridges: A:R.122 SO4.6: 5 residues within 4Å: Chain A: N.117, R.122 Chain C: N.117, R.122 Ligands: SO4.12 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.117, C:N.117, A:N.117 Water bridges: C:Y.119, C:R.122, A:Y.119, A:R.122 Salt bridges: C:R.122, A:R.122 SO4.11: 3 residues within 4Å: Chain C: R.122, K.123 Ligands: NAG-NAG-MAN-MAN-FUC-FUC.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:G.197 Hydrogen bonds: C:K.123 Salt bridges: C:R.122 SO4.12: 5 residues within 4Å: Chain A: N.117, R.122 Chain C: N.117, R.122 Ligands: SO4.6 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:N.117, A:N.117, A:N.117 Water bridges: C:Y.119, C:R.122, A:Y.119, A:R.122 Salt bridges: C:R.122, A:R.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Crystal structure of earthworm fibrinolytic enzyme component B: a novel, glycosylated two-chained trypsin. J.Mol.Biol. (2005)

Release Date

2005-04-19

Peptides

fibrinotic enzyme component B: AC
fibrinotic enzyme component B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

fibrinotic enzyme component B

fibrinotic enzyme component B

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