SMTL ID : 1n1m.1

Human Dipeptidyl Peptidase IV/CD26 in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAG-NDG-FUC.1: 7 residues within 4Å: Chain A: E.29, V.40, N.42, Y.45, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.45 Hydrogen bonds: A:N.42, A:N.47 Water bridges: A:E.29, A:E.29

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.2: 4 residues within 4Å: Chain A: R.109, I.110, P.111, N.112 No protein-ligand interaction detected (PLIP)

4 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: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:E.294, A:E.294 NAG-NAG.5: 4 residues within 4Å: Chain A: R.146, W.149, V.241, N.243 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.149 NAG-NAG.6: 5 residues within 4Å: Chain A: I.281, N.283, S.311, T.312, D.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.640 NAG-NAG.8: 6 residues within 4Å: Chain B: N.181, T.183, N.234, Q.270, E.271, E.294 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.234, B:N.234, B:E.294, B:E.294 Water bridges: B:E.294

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

NAG-NDG-MAN.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, K.229 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194 Water bridges: A:E.194, A:E.194, A:K.229

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

NAG-FUC.7: 5 residues within 4Å: Chain B: V.40, Y.45, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.47 Hydrogen bonds: B:S.49

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

NAG-NAG-BMA.9: 5 residues within 4Å: Chain B: T.150, I.156, N.191, T.193, E.194 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.193 NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: W.149, T.150, N.243 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.150

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

NAG-NDG.11: 7 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, R.558, D.640 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.283

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

NAG.12: 3 residues within 4Å: Chain A: N.482, R.543, D.567 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.543, A:R.543, A:D.567 NAG.16: 3 residues within 4Å: Chain B: R.109, P.111, N.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.112 NAG.17: 3 residues within 4Å: Chain B: N.482, R.543, D.567 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.482, B:R.543

4 x HG: MERCURY (II) ION(Non-covalent)

HG.13: 3 residues within 4Å: Chain A: F.319, C.513, Y.547 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.513, A:C.513 HG.14: 4 residues within 4Å: Chain A: V.169, C.263, L.278, P.321 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.263, H2O.18 HG.18: 3 residues within 4Å: Chain B: C.263, L.278, P.321 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.263, H2O.34 HG.19: 3 residues within 4Å: Chain B: F.319, C.513, Y.547 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.513

2 x A3M: 2-AMINO-3-METHYL-1-PYRROLIDIN-1-YL-BUTAN-1-ONE(Non-covalent)

A3M.15: 11 residues within 4Å: Chain A: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:Y.624, A:Y.624, A:N.672 Water bridges: A:S.592 A3M.20: 12 residues within 4Å: Chain B: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.593, B:V.618, B:W.621 Hydrogen bonds: B:R.87, B:E.167, B:Y.624, B:N.672

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rasmussen, H.B. et al., Crystal structure of human dipeptidyl peptidase IV/CD26 in complex with a substrate analogue. Nat.Struct.Biol. (2003)

Release Date

2002-12-27

Peptides

Dipeptidyl peptidase IV SOLUBLE FORM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase IV SOLUBLE FORM

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