SMTL ID : 6sgp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

8 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: 4 residues within 4Å: Chain A: N.33, Q.36, Q.52, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.52 NAG-NAG.2: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 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.4: 2 residues within 4Å: Chain A: N.152, S.154 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.33, Q.36, Q.52, Q.56 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.52 NAG-NAG.18: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: N.152, S.154 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.5: 7 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608, D.609, K.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.608, A:K.612 NAG-NAG-BMA-MAN.21: 7 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608, D.609, K.612 2 PLIP interactions: 2 interactions with chain B 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.6: 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:H.69 Water bridges: B:H.69 NAG-NAG-BMA-MAN-MAN.22: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:H.69 Water bridges: A:H.69

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

NAG.7: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 5 PLIP interactions: 5 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 NAG.23: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 5 PLIP interactions: 5 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

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.9, LDK.15 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.5 ZN.9: 7 residues within 4Å: Chain A: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.8, LDK.15 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.5 ZN.24: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.25, LDK.31 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.21 ZN.25: 7 residues within 4Å: Chain B: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.24, LDK.31 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.21

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.26: 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.11: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 14 residues within 4Å: Chain A: D.326, R.327, R.397, E.401, R.402, R.619, M.626, F.627 Chain B: R.327, D.623, Q.624, F.627, T.702 Ligands: PGE.28 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.327, A:R.327, A:R.397, A:R.402 Water bridges: B:Q.624, B:Q.624 PGE.28: 14 residues within 4Å: Chain A: R.327, D.623, Q.624, F.627, T.702 Chain B: D.326, R.327, R.397, E.401, R.402, R.619, M.626, F.627 Ligands: PGE.12 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:Q.624, A:Q.624 Hydrogen bonds: B:R.327, B:R.327, B:R.397, B:R.402

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

PEG.13: 3 residues within 4Å: Chain A: D.566, Y.569, F.590 No protein-ligand interaction detected (PLIP) PEG.14: 1 residues within 4Å: Chain A: Y.32 No protein-ligand interaction detected (PLIP) PEG.29: 3 residues within 4Å: Chain B: D.566, Y.569, F.590 No protein-ligand interaction detected (PLIP) PEG.30: 1 residues within 4Å: Chain B: Y.32 No protein-ligand interaction detected (PLIP)

2 x LDK: (2~{S})-2-[[(2~{S})-1,5-bis(oxidanyl)-1,5-bis(oxidanylidene)pentan-2-yl]sulfamoylamino]pentanedioic acid(Non-covalent)

LDK.15: 18 residues within 4Å: Chain A: R.167, N.214, D.344, M.381, E.382, G.384, L.385, D.410, G.475, N.476, R.491, R.493, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, ZN.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.657 Hydrogen bonds: A:N.214, A:G.475, A:N.476, A:Y.509, A:Y.657 Water bridges: A:N.214, A:R.493, A:K.656 Salt bridges: A:R.167, A:R.420, A:R.491, A:R.493, A:H.510, A:K.656 LDK.31: 18 residues within 4Å: Chain B: R.167, N.214, D.344, M.381, E.382, G.384, L.385, D.410, G.475, N.476, R.491, R.493, Y.509, H.510, K.656, Y.657 Ligands: ZN.24, ZN.25 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.657 Hydrogen bonds: B:N.214, B:G.475, B:N.476, B:Y.509, B:Y.657 Water bridges: B:N.214, B:R.493, B:K.656 Salt bridges: B:R.167, B:R.420, B:R.491, B:R.493, B:H.510, B:K.656

2 x NA: SODIUM ION(Non-functional Binders)

NA.16: 3 residues within 4Å: Chain A: P.230, N.232, E.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.232, A:E.394 NA.32: 3 residues within 4Å: Chain B: P.230, N.232, E.394 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.232, B:E.394

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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