SMTL ID : 3rbu.1

N-terminally AviTEV-tagged Human Glutamate Carboxypeptidase II in complex with 2-PMPA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: N.65, Q.68, Q.84, S.87, Q.88 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: Y.116, E.126, I.127, F.128, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.65, Q.68, Q.84, S.87, Q.88 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: Y.116, E.126, I.127, F.128, N.129 No protein-ligand interaction detected (PLIP)

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(Post Translational Modification)

NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: S.461, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.640 Water bridges: A:R.587, A:R.587, A:Q.640, A:Q.640 NAG-NAG-BMA.15: 4 residues within 4Å: Chain B: S.461, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.640 Water bridges: B:R.587, B:R.587, B:Q.640, B:Q.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.4: 9 residues within 4Å: Chain A: S.620, S.623, A.624, N.627, Q.729 Chain B: H.101, E.265, Y.266, R.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.343, B:R.343, B:R.343 Water bridges: B:H.101, B:R.343, B:R.343, B:R.343 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: H.101, E.265, Y.266, R.343 Chain B: S.620, S.623, A.624, N.627, Q.729 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.343, A:R.343, A:R.343 Water bridges: A:H.101, A:R.343, A:R.343, A:R.343

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

NAG.5: 4 residues within 4Å: Chain A: N.110, T.112, H.113, T.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.110 Water bridges: A:Q.156 NAG.6: 2 residues within 4Å: Chain A: N.184, S.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.186 NAG.7: 4 residues within 4Å: Chain A: W.235, N.448, F.554, Y.555 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.235, A:Y.555 Hydrogen bonds: A:W.235, A:F.554 Water bridges: A:N.448 NAG.17: 4 residues within 4Å: Chain B: N.110, T.112, H.113, T.338 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.110 Water bridges: B:Q.156 NAG.18: 2 residues within 4Å: Chain B: N.184, S.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.186 NAG.19: 4 residues within 4Å: Chain B: W.235, N.448, F.554, Y.555 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.235, B:Y.555 Hydrogen bonds: B:W.235, B:F.554 Water bridges: B:N.448

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.376, E.414, H.542 Ligands: ZN.9, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.376, A:E.414, A:E.414, A:H.542 ZN.9: 7 residues within 4Å: Chain A: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.8, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.366, A:D.376, A:D.442, A:D.442 ZN.20: 5 residues within 4Å: Chain B: D.376, E.414, H.542 Ligands: ZN.21, G88.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.376, B:E.414, B:E.414, B:H.542 ZN.21: 7 residues within 4Å: Chain B: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.20, G88.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.366, B:D.376, B:D.442, B:D.442

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.258, A:Y.261, A:E.422, A:E.422, A:E.425 CA.22: 4 residues within 4Å: Chain B: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.258, B:Y.261, B:E.422, B:E.422, B:E.425

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 5 residues within 4Å: Chain A: N.440, D.442, R.523, R.525, R.569 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: N.440, D.442, R.523, R.525, R.569 Ligand excluded by PLIP

2 x G88: (2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID(Non-covalent)

G88.12: 17 residues within 4Å: Chain A: R.199, N.246, H.366, D.376, E.413, E.414, G.416, L.417, D.442, G.507, N.508, Y.541, H.542, K.688, Y.689 Ligands: ZN.8, ZN.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.417 Hydrogen bonds: A:N.246, A:E.414, A:G.507, A:N.508, A:Y.541, A:Y.541, A:Y.689 Salt bridges: A:R.199, A:H.542, A:K.688 G88.24: 17 residues within 4Å: Chain B: R.199, N.246, H.366, D.376, E.413, E.414, G.416, L.417, D.442, G.507, N.508, Y.541, H.542, K.688, Y.689 Ligands: ZN.20, ZN.21 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.417 Hydrogen bonds: B:N.246, B:E.413, B:E.414, B:G.507, B:N.508, B:Y.541, B:Y.541, B:Y.689 Water bridges: B:E.414 Salt bridges: B:R.199, B:H.542, B:K.688

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tykvart, J. et al., Efficient and versatile one-step affinity purification of in vivo biotinylated proteins: Expression, characterization and structure analysis of recombinant human glutamate carboxypeptidase II. Protein Expr.Purif. (2012)

Release Date

2012-01-04

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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