SMTL ID : 5hvf.1

Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-i83)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 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.1: 5 residues within 4Å: Chain A: R.15, V.19, N.22, T.26, H.61 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: E.28, N.51, S.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.51, A:S.53 NAG.3: 5 residues within 4Å: Chain A: N.63 Chain B: V.54, G.55, S.56, T.57 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.54 Hydrogen bonds: B:S.56, B:S.56 NAG.4: 5 residues within 4Å: Chain A: Q.82, N.86, V.89, Q.100, E.376 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.159, E.162, H.288 Ligands: FLC.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.159, A:E.162, A:E.162

1 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 13 residues within 4Å: Chain A: H.159, E.162, R.217, N.234, R.235, H.288, S.289, S.299, L.340, Y.341, A.343, E.363 Ligands: ZN.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.234, A:S.299, A:Y.341, A:Y.341, A:Y.341, A:E.363 Salt bridges: A:H.159, A:H.159, A:R.217, A:R.217, A:R.235, A:R.235, 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-i83: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carboxypeptidase B2

VHH-i83

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