SMTL ID : 5hvg.1 (1 other biounit)

Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-a204)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.22, T.26, Y.27, H.61 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: E.28, N.51, A.52, S.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.28, A:E.28, A:N.51, A:S.53, A:S.53 NAG.3: 1 residues within 4Å: Chain A: N.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.63 NAG.4: 5 residues within 4Å: Chain A: N.86, V.89, S.96, Q.100, E.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.100, A:E.376

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.159, E.162, H.288 Ligands: ACT.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.159, A:E.162, A:E.162, A:H.288

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: H.159, E.162, R.217, H.288, S.289, E.363 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.289 Salt bridges: A:H.159, A:R.217, A:H.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, X. et al., Elucidation of the molecular mechanisms of two nanobodies that inhibit thrombin-activatable fibrinolysis inhibitor activation and activated thrombin-activatable fibrinolysis inhibitor activity. J.Thromb.Haemost. (2016)

Release Date

2016-06-22

Peptides

Carboxypeptidase B2: A
VHH-a204: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carboxypeptidase B2

VHH-a204

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