SMTL ID : 1r9m.1 (3 other biounits)

Crystal Structure of Human Dipeptidyl Peptidase IV at 2.1 Ang. Resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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.1: 2 residues within 4Å: Chain A: I.115, N.117 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: W.154, N.248 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.154 NAG-NAG.4: 6 residues within 4Å: Chain A: I.286, N.288, M.315, S.316, T.317, R.563 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: N.186, T.188, N.239, D.241, Q.275, E.276, E.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.239, B:N.239, B:E.299 NAG-NAG.6: 4 residues within 4Å: Chain B: I.161, N.196, T.198, E.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.199

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

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: I.161, N.196, T.198, E.199 No protein-ligand interaction detected (PLIP)

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

NAG.7: 6 residues within 4Å: Chain A: V.45, N.47, Y.50, N.52, S.53, S.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.45 NAG.8: 4 residues within 4Å: Chain A: N.186, T.188, Q.275, E.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.186, A:N.186, A:E.276, A:E.276 NAG.9: 6 residues within 4Å: Chain A: L.486, N.487, T.489, F.491, R.548, D.572 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.489, A:R.548, A:R.548 NAG.10: 3 residues within 4Å: Chain A: D.648, R.651, N.652 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.651 Hydrogen bonds: A:D.648, A:D.648 NAG.11: 4 residues within 4Å: Chain B: V.45, N.52, S.53, S.54 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.45 Hydrogen bonds: B:N.52, B:S.54 NAG.12: 5 residues within 4Å: Chain B: R.114, I.115, P.116, N.117 Ligands: FUC.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.114 Hydrogen bonds: B:R.114 NAG.14: 2 residues within 4Å: Chain B: W.154, N.248 No protein-ligand interaction detected (PLIP) NAG.15: 5 residues within 4Å: Chain B: I.286, N.288, S.316, T.317, R.563 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.288, B:N.288, B:R.563 NAG.16: 6 residues within 4Å: Chain B: L.486, N.487, T.489, F.491, R.548, D.572 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.489, B:R.548, B:R.548, B:D.572 NAG.17: 3 residues within 4Å: Chain B: D.648, R.651, N.652 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.651 Hydrogen bonds: B:D.648

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.13: 1 residues within 4Å: Ligands: NAG.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aertgeerts, K. et al., Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation. Protein Sci. (2004)

Release Date

2004-06-29

Peptides

Dipeptidyl peptidase IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase IV

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