SMTL ID : 4twe.1

Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like protein (NAALADaseL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: T.161, Q.163, N.337, S.339, Y.341 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: I.491, R.492, Y.493, N.495, L.503, S.537 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.537, A:S.537 NAG-NAG.4: 6 residues within 4Å: Chain B: N.454, P.479, K.559, F.560, P.563 Ligands: GOL.26 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: I.491, R.492, Y.493, N.495, L.503 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537

1 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.2: 6 residues within 4Å: Chain A: N.454, P.479, F.560, P.563, S.566 Ligands: GOL.14 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: D.381, E.420, Y.547, H.548 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.381, A:E.420, A:E.420, A:H.548 ZN.7: 6 residues within 4Å: Chain A: H.371, D.381, E.419, E.420, D.448 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.371, A:D.381, A:D.448, A:D.448 ZN.17: 5 residues within 4Å: Chain B: D.381, E.420, Y.547, H.548 Ligands: ZN.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.381, B:E.420, B:E.420, B:H.548 ZN.18: 6 residues within 4Å: Chain B: H.371, D.381, E.419, E.420, D.448 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.371, B:D.381, B:D.448, B:D.448

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: T.261, L.264, E.428, E.431, Y.680 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.261, A:E.428, A:E.431, A:E.431, H2O.6 CA.19: 5 residues within 4Å: Chain B: T.261, L.264, E.428, E.431, Y.680 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.261, B:E.428, B:E.431, B:E.431, H2O.35

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

NAG.9: 5 residues within 4Å: Chain A: N.139, G.142, Q.144, G.145, G.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.139, A:Q.144 NAG.10: 2 residues within 4Å: Chain A: N.302, G.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.302, A:G.303 Water bridges: A:N.302, A:G.303, A:G.303 NAG.11: 4 residues within 4Å: Chain A: E.106, L.346, R.347, N.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.106, A:N.348 Water bridges: A:N.348 NAG.20: 4 residues within 4Å: Chain B: N.139, G.142, G.145, G.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.139, B:Q.144 NAG.21: 2 residues within 4Å: Chain B: N.302, G.303 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.302, B:G.303, B:G.303 Water bridges: B:N.302, B:N.302, B:R.319 NAG.22: 4 residues within 4Å: Chain B: T.161, Q.163, N.337, S.339 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.163 Hydrogen bonds: B:T.161, B:T.161, B:S.339 Water bridges: B:Q.163 NAG.23: 4 residues within 4Å: Chain B: E.106, L.346, R.347, N.348 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.106 Hydrogen bonds: B:E.106, B:E.106, B:N.348 Water bridges: B:E.106, B:N.348

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: Y.255, S.279, P.676, E.677, E.678, R.679 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.279, A:S.279, A:E.677, A:R.679 Water bridges: A:Y.263, A:E.678 GOL.13: 6 residues within 4Å: Chain A: S.75, S.76, F.111, R.343, E.345, R.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.343, A:E.345 Water bridges: A:R.347, A:R.347 GOL.14: 4 residues within 4Å: Chain A: W.240, Y.534, F.560 Ligands: NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.560 Water bridges: A:F.560 GOL.24: 5 residues within 4Å: Chain B: S.76, F.111, R.343, E.345, R.347 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.343, B:E.345 GOL.25: 8 residues within 4Å: Chain A: Y.365, F.429, F.433, K.436, L.437 Chain B: V.740, D.742, L.743 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.436 Water bridges: B:D.742 GOL.26: 6 residues within 4Å: Chain B: W.240, A.453, Y.534, F.560, L.561 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.560 GOL.27: 6 residues within 4Å: Chain B: Y.255, S.279, P.676, E.677, E.678, R.679 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.279, B:S.279, B:E.678, B:R.679, B:R.679 Water bridges: B:Y.263

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 5 residues within 4Å: Chain A: Y.196, G.200, R.201, E.248, R.542 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.201, A:R.201, A:R.201, A:E.248, A:R.542, A:R.542 Water bridges: A:G.202, A:S.251, A:Y.547 PEG.16: 7 residues within 4Å: Chain A: P.40, Q.41, V.360, R.408, F.586, P.652 Chain B: L.653 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.360 Hydrogen bonds: A:Q.41, A:R.408, A:R.408 Water bridges: A:E.361 PEG.28: 5 residues within 4Å: Chain B: Y.196, G.200, R.201, E.248, R.542 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.201, B:R.201, B:R.201, B:E.248, B:S.251, B:R.542 Water bridges: B:G.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tykvart, J. et al., Structural and biochemical characterization of a novel aminopeptidase from human intestine. J.Biol.Chem. (2015)

Release Date

2015-03-18

Peptides

N-acetylated-alpha-linked acidic dipeptidase-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylated-alpha-linked acidic dipeptidase-like protein