SMTL ID : 3dgv.1 (3 other biounits)

Crystal structure of thrombin activatable fibrinolysis inhibitor (TAFI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.1: 4 residues within 4Å: Chain A: R.3, N.51, A.52, S.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.51, A:S.53, A:S.53, A:R.3 Water bridges: A:R.3, A:N.51 NAG-NDG.6: 2 residues within 4Å: Chain B: N.63, A.64 No protein-ligand interaction detected (PLIP)

1 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.2: 1 residues within 4Å: Chain A: N.63 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.64

2 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: 5 residues within 4Å: Chain A: Q.82, S.85, N.86, I.89, E.376 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: R.81, Q.82, S.85, N.86, I.89, Q.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.81, B:R.81

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.4: 4 residues within 4Å: Chain A: Q.18, I.19, N.22, T.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22

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

NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: R.3, K.28, N.51, A.52, S.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.3

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: H.159, E.162, H.288 Ligands: MLI.18 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.159, A:E.162, A:E.162, A:H.288 ZN.20: 4 residues within 4Å: Chain B: H.159, E.162, H.288 Ligands: MLI.32 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.159, B:E.162, B:E.162, B:H.288

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

SO4.9: 6 residues within 4Å: Chain A: K.225, N.226, A.227, S.249, S.250, S.251 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: K.240, H.241, Y.300, S.301, S.303 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: Y.44, E.45 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: H.308, S.312, R.316 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: H.223, E.224 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: T.13, R.15, Q.16, R.66 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: T.13, S.14, K.42 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: H.126, G.128, S.129 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: I.325, H.326, R.327, N.328 Chain B: K.369 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: K.225, N.226, A.227, S.250, S.251 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: R.330 Chain B: Y.44, E.45 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: H.223, E.224 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: T.13, S.14, K.42 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: K.240, H.241, Y.300, S.301, S.303 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: K.369 Chain B: I.325, H.326, R.327, N.328 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: H.308, S.312, R.316, E.338 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: R.330 Chain B: R.330, K.367 Ligands: SO4.29 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain A: T.332, K.367 Chain B: R.330 Ligands: SO4.28 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: T.13, R.15, Q.16, R.66 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain A: K.399 Chain B: R.12, R.66 Ligand excluded by PLIP

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.18: 8 residues within 4Å: Chain A: H.159, E.162, R.217, N.234, R.235, H.288, E.363 Ligands: ZN.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.217 Salt bridges: A:H.159, A:H.159, A:R.217, A:R.235, A:H.288 MLI.32: 8 residues within 4Å: Chain B: H.159, E.162, R.217, N.234, R.235, H.288, E.363 Ligands: ZN.20 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.234 Water bridges: B:Y.290 Salt bridges: B:H.159, B:H.159, B:R.217, B:R.235, B:H.288

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

NAG.19: 2 residues within 4Å: Chain B: N.22, T.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.22 Water bridges: B:N.22, B:N.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, K. et al., The crystal structure of thrombin-activable fibrinolysis inhibitor (TAFI) provides the structural basis for its intrinsic activity and the short half-life of TAFIa. J.Biol.Chem. (2008)

Release Date

2008-07-22

Peptides

Carboxypeptidase B2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carboxypeptidase B2

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