SMTL ID : 1r9m.4 (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-tetramer

Ligands

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.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 NAG-NAG.19: 4 residues within 4Å: Chain D: I.161, N.196, T.198, E.199 No protein-ligand interaction detected (PLIP)

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)

21 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 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.186, T.188, Q.275, E.276 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: L.486, N.487, T.489, F.491, R.548, D.572 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: D.648, R.651, N.652 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain B: V.45, N.52, S.53, S.54 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain B: R.114, I.115, P.116, N.117 Ligands: FUC.13 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: W.154, N.248 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain B: I.286, N.288, S.316, T.317, R.563 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain B: L.486, N.487, T.489, F.491, R.548, D.572 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: D.648, R.651, N.652 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: R.114, I.115, N.117 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: N.186, T.188, Q.275, E.276 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: W.154, N.248 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain C: I.286, N.288, M.315, S.316, T.317, R.563 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain C: L.486, N.487, F.491, R.548, D.572, E.575 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: R.114, I.115, P.116, N.117 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain D: N.186, T.188, Q.275, E.276 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: W.154, V.246, N.248 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain D: I.286, N.288, S.316, T.317, R.563 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain D: L.486, N.487, T.489, F.491, R.548, D.572 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: D.648, N.652 Ligand excluded by PLIP

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

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

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.18: 5 residues within 4Å: Chain C: I.161, N.196, T.198, E.199, K.234 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dipeptidyl peptidase IV

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