SMTL ID : 2bgr.1

Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MET- ASP- PRO: HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE(Non-covalent)

MET-ASP-PRO.1: 10 residues within 4Å: Chain A: R.97, E.177, E.178, Y.519, S.602, Y.603, V.628, Y.634, Y.638, H.712 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.638 Hydrogen bonds: A:E.177, A:S.602, A:Y.634, A:Y.634 Water bridges: A:R.97, A:R.97 Salt bridges: A:R.97, A:H.712 MET-ASP-PRO.2: 10 residues within 4Å: Chain B: R.97, E.177, E.178, Y.519, S.602, Y.603, V.628, Y.634, Y.638, H.712 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.638 Hydrogen bonds: B:R.97, B:E.177, B:Y.519, B:Y.519, B:S.602, B:Y.634 Salt bridges: B:H.712

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

NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: E.39, V.50, N.52, Y.55, N.57, S.58, S.59 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 7 residues within 4Å: Chain A: N.191, T.193, F.194, Q.280, E.281, Y.302, E.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.194, A:Y.302 Hydrogen bonds: A:E.281, A:E.304 NAG-NAG.6: 3 residues within 4Å: Chain A: W.159, V.251, N.253 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain A: I.291, N.293, M.320, S.321, T.322, R.568, E.649, D.650 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: N.191, T.193, F.194, N.244, Q.280, E.281, Y.302, E.304 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.194, B:Y.302 Hydrogen bonds: B:E.304 Water bridges: B:E.304 NAG-NAG.11: 3 residues within 4Å: Chain B: W.159, T.160, N.253 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.160 NAG-NAG.12: 6 residues within 4Å: Chain B: I.291, N.293, S.321, T.322, R.568, D.650 No protein-ligand interaction detected (PLIP)

2 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(Post Translational Modification)

NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: I.166, N.201, T.203, E.204 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain B: I.166, N.201, T.203, E.204 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.8: 7 residues within 4Å: Chain B: E.39, V.50, N.52, Y.55, N.57, S.58, S.59 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.55, B:N.57 Hydrophobic interactions: B:V.50 Water bridges: B:E.39, B:N.52, B:S.58

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

NAG.13: 3 residues within 4Å: Chain A: R.119, I.120, N.122 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.119 Hydrogen bonds: A:N.122, A:N.122 NAG.14: 4 residues within 4Å: Chain A: E.45, N.46, N.47, N.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.45, A:N.46, A:N.47, A:N.64 NAG.15: 3 residues within 4Å: Chain B: R.119, I.120, N.122 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.119 Hydrogen bonds: B:R.119, B:R.119 Water bridges: B:N.122, B:N.122 NAG.16: 4 residues within 4Å: Chain B: E.45, N.46, N.47, N.64 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.46 Hydrogen bonds: B:N.46, B:N.47, B:N.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weihofen, W.A. et al., Crystal Structures of HIV-1 Tat-Derived Nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase Iv (Cd26). J.Biol.Chem. (2005)

Release Date

2005-01-27

Peptides

DIPEPTIDYL PEPTIDASE IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIPEPTIDYL PEPTIDASE IV