SMTL ID : 1qmu.1

Duck carboxypeptidase D domain II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

6 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.1: 7 residues within 4Å: Chain A: T.129, N.133, N.137, Y.138, D.139, R.142, D.153 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.142 NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: F.306, L.308, Q.372, N.374 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 7 residues within 4Å: Chain B: T.129, N.133, N.137, Y.138, D.139, R.142, D.153 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.142 NAG-NAG-MAN.10: 4 residues within 4Å: Chain B: F.306, L.308, Q.372, N.374 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 7 residues within 4Å: Chain C: T.129, N.133, N.137, Y.138, D.139, R.142, D.153 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.142 NAG-NAG-MAN.17: 4 residues within 4Å: Chain C: F.306, L.308, Q.372, N.374 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.318, T.320 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.318, T.320 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.318, T.320 No protein-ligand interaction detected (PLIP)

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: K.220, C.227, K.228, D.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.228 Water bridges: A:K.228, A:D.229, A:D.229 Salt bridges: A:K.220 SO4.5: 2 residues within 4Å: Chain A: R.289, R.290 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.289, A:R.290 SO4.6: 7 residues within 4Å: Chain A: H.71, R.132, N.141, R.142, Y.247, V.249 Ligands: ZN.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.141, A:Y.247 Water bridges: A:E.74, A:Y.247 Salt bridges: A:H.71, A:R.132, A:R.142, A:H.178 SO4.11: 4 residues within 4Å: Chain B: K.220, C.227, K.228, D.229 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.228 Water bridges: B:K.228, B:D.229, B:D.229 Salt bridges: B:K.220 SO4.12: 2 residues within 4Å: Chain B: R.289, R.290 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.289, B:R.290 SO4.13: 7 residues within 4Å: Chain B: H.71, R.132, N.141, R.142, Y.247, V.249 Ligands: ZN.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.141 Water bridges: B:E.74, B:Y.247 Salt bridges: B:H.71, B:R.132, B:R.142, B:H.178 SO4.18: 4 residues within 4Å: Chain C: K.220, C.227, K.228, D.229 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.228, C:D.229 Water bridges: C:K.228, C:D.229, C:D.229 Salt bridges: C:K.220 SO4.19: 2 residues within 4Å: Chain C: R.289, R.290 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.289, C:R.290 SO4.20: 7 residues within 4Å: Chain C: H.71, R.132, N.141, R.142, Y.247, V.249 Ligands: ZN.21 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.141 Water bridges: C:E.74, C:Y.247 Salt bridges: C:H.71, C:R.132, C:R.142, C:H.178

3 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: H.71, E.74, R.132, H.178, E.269 Ligands: SO4.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.71, A:E.74, A:E.74, A:H.178, H2O.5 ZN.14: 6 residues within 4Å: Chain B: H.71, E.74, R.132, H.178, E.269 Ligands: SO4.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.71, B:E.74, B:E.74, B:H.178, H2O.10 ZN.21: 6 residues within 4Å: Chain C: H.71, E.74, R.132, H.178, E.269 Ligands: SO4.20 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.71, C:E.74, C:E.74, C:H.178, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomis-Rueth, F.X. et al., Crystal Structure of Avian Carboxypeptidase D Domain II : A Prototype for the Regulatory Metallocarboxypeptidase Subfamily. Embo J. (1999)

Release Date

2000-10-13

Peptides

CARBOXYPEPTIDASE GP180 RESIDUES 503-882: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

CARBOXYPEPTIDASE GP180 RESIDUES 503-882

Related Entries With Identical Sequence