SMTL ID : 6skh.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor sulfamide inhibitor GluAsp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: N.33, Q.36, Q.52, S.55, Q.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.52 Water bridges: A:S.55 NAG-NAG-BMA.20: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.52 Water bridges: B:S.55

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.2: 5 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 Ligands: BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 Ligands: BMA.32 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.4: 7 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608, D.609, K.612 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.608, A:K.612 Hydrogen bonds: A:Q.608, A:K.612 NAG-NAG-BMA-MAN.23: 7 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608, D.609, K.612 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.608, B:K.612 Hydrogen bonds: B:Q.608, B:K.612

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.5: 10 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: L.67, H.69, E.233, Y.234, R.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:L.67, B:H.69 Water bridges: B:H.69, B:L.67 NAG-NAG-BMA-MAN-MAN.24: 10 residues within 4Å: Chain A: L.67, H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:L.67, A:H.69 Water bridges: A:H.69, A:L.67

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

NAG.6: 2 residues within 4Å: Chain A: N.152, S.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.152, A:S.154 NAG.7: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 Water bridges: A:N.416, A:N.416 NAG.25: 2 residues within 4Å: Chain B: N.152, S.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.152, B:S.154 NAG.26: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522 Water bridges: B:N.416, B:N.416

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 1 residues within 4Å: Chain A: R.468 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: Y.569, F.590 No protein-ligand interaction detected (PLIP) EDO.16: 1 residues within 4Å: Chain A: Y.32 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain A: P.461, E.462, F.463, S.464 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.464, A:S.464 EDO.27: 1 residues within 4Å: Chain B: R.468 No protein-ligand interaction detected (PLIP) EDO.34: 2 residues within 4Å: Chain B: Y.569, F.590 No protein-ligand interaction detected (PLIP) EDO.35: 1 residues within 4Å: Chain B: Y.32 No protein-ligand interaction detected (PLIP) EDO.36: 4 residues within 4Å: Chain B: P.461, E.462, F.463, S.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.464, B:S.464

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.10, LHK.18 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510, H2O.12 ZN.10: 7 residues within 4Å: Chain A: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.9, LHK.18 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410, H2O.12 ZN.28: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.29, LHK.37 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510, H2O.35 ZN.29: 7 residues within 4Å: Chain B: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.28, LHK.37 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410, H2O.35

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 4 residues within 4Å: Chain A: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393 CA.30: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.226, B:Y.229, B:E.390, B:E.390, B:E.393

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

CL.12: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

2 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.13: 1 residues within 4Å: Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) BMA.32: 1 residues within 4Å: Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP)

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

PEG.14: 8 residues within 4Å: Chain A: E.701, S.704, E.705, V.706 Chain B: Y.328, L.374, W.391, L.398 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.701 Water bridges: A:S.704, B:N.395 PEG.33: 8 residues within 4Å: Chain A: Y.328, L.374, W.391, L.398 Chain B: E.701, S.704, E.705, V.706 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.701 Water bridges: B:S.704, A:N.395

2 x LHK: (2~{S})-2-[[(2~{S})-1,4-bis(oxidanyl)-1,4-bis(oxidanylidene)butan-2-yl]sulfamoylamino]pentanedioic acid(Non-covalent)

LHK.18: 22 residues within 4Å: Chain A: F.166, R.167, N.214, D.344, M.381, E.382, G.384, L.385, D.410, S.411, G.475, N.476, R.491, R.493, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.9, ZN.10, GOL.19 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.509 Hydrogen bonds: A:N.214, A:D.410, A:S.411, A:S.411, A:G.475, A:G.475, A:G.475, A:N.476 Water bridges: A:N.214, A:R.491, A:R.491, A:R.491, A:R.491, A:R.493, A:R.493, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:R.493, A:H.510, A:K.656 LHK.37: 22 residues within 4Å: Chain B: F.166, R.167, N.214, D.344, M.381, E.382, G.384, L.385, D.410, S.411, G.475, N.476, R.491, R.493, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.28, ZN.29, GOL.38 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.509 Hydrogen bonds: B:N.214, B:D.410, B:S.411, B:S.411, B:G.475, B:G.475, B:G.475, B:N.476 Water bridges: B:N.214, B:R.491, B:R.491, B:R.491, B:R.491, B:R.493, B:R.493, B:K.656 Salt bridges: B:R.167, B:R.491, B:R.493, B:R.493, B:H.510, B:K.656

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 3 residues within 4Å: Chain A: Y.509, Y.657 Ligands: LHK.18 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.414, A:Y.509 Water bridges: A:R.420, A:S.474, A:R.491, A:R.491, A:R.493, A:Y.657 GOL.38: 3 residues within 4Å: Chain B: Y.509, Y.657 Ligands: LHK.37 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.414, B:Y.509 Water bridges: B:R.420, B:S.474, B:R.491, B:R.491, B:R.493, B:Y.657

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Novakova, Z. et al., Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. J.Chem.Inf.Model. (2024)

Release Date

2020-08-26

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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