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

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MET- TRP- PRO- VAL- ASP- PRO: TAT PROTEIN(Non-covalent)

MET-TRP-PRO-VAL-ASP-PRO.1: 12 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:W.591, A:Y.624, A:Y.628 Hydrogen bonds: A:R.87, A:Y.509, A:Y.624 MET-TRP-PRO-VAL-ASP-PRO.2: 11 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.624, B:Y.628 Hydrogen bonds: B:R.87, B:Y.509, B:S.592, B:Y.624, B:Y.624 pi-Stacking: B:Y.509

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.3: 6 residues within 4Å: Chain A: E.29, N.42, Y.45, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.45

5 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: 4 residues within 4Å: Chain A: Y.80, R.109, I.110, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: N.181, T.183, N.234, Q.270, E.271, Y.292, E.294 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.183 NAG-NAG.7: 5 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, R.558 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain B: N.181, T.183, Q.270, E.271, Y.292, E.294 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 9 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, N.557, R.558, E.639, D.640 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.558, B:R.558, B:D.640

2 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(Post Translational Modification)

NAG-NAG-BMA-MAN.6: 8 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 Chain C: R.33, R.34, G.35, I.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.35 NAG-NAG-BMA-MAN.10: 7 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 Chain D: R.33, R.34, G.35 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.35

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

NAG-FUL.8: 7 residues within 4Å: Chain B: E.29, V.40, N.42, Y.45, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.49, B:S.49

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

NAG.12: 3 residues within 4Å: Chain A: W.149, V.241, N.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.243 NAG.13: 4 residues within 4Å: Chain A: L.481, N.482, F.486, R.543 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.482, A:R.543, A:R.543 NAG.14: 4 residues within 4Å: Chain A: E.35, N.36, N.37, N.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.35, A:N.36, A:N.37, A:N.54 NAG.15: 2 residues within 4Å: Chain B: R.109, N.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.109, B:N.112 NAG.16: 2 residues within 4Å: Chain B: W.149, N.243 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.243 NAG.17: 3 residues within 4Å: Chain B: N.482, R.543, D.567 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.543, B:R.543, B:D.567 NAG.18: 3 residues within 4Å: Chain B: E.35, N.37, N.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.35, B:E.35, B:N.37

2 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain C: H.15, H.17, H.214, H.238, D.295 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.15, C:H.17, C:H.214, C:D.295 ZN.20: 5 residues within 4Å: Chain D: H.15, H.17, H.214, H.238, D.295 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.15, D:H.17, D:H.214, D:D.295

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
ADENOSINE DEAMINASE: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
G

D
H

DIPEPTIDYL PEPTIDASE IV

ADENOSINE DEAMINASE

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