SMTL ID : 6rti.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 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: 4 residues within 4Å: Chain A: N.33, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain C: E.233, Y.234, R.311 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.233 NAG-NAG-BMA.20: 4 residues within 4Å: Chain C: N.33, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain C: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 8 residues within 4Å: Chain A: E.233, Y.234, R.311 Chain C: S.588, S.591, A.592, N.595, Q.697 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.233

6 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: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.152, S.154 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: W.203, N.416, F.522, Y.523 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: 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: 4 residues within 4Å: Chain A: S.429, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.608, A:Q.608 NAG-NAG-BMA-MAN.24: 4 residues within 4Å: Chain C: S.429, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.608, C:Q.608

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.9, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.9: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.8, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410 ZN.27: 6 residues within 4Å: Chain C: D.344, E.382, Y.509, H.510 Ligands: ZN.28, G88.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.344, C:E.382, C:E.382, C:H.510 ZN.28: 7 residues within 4Å: Chain C: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.27, G88.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.334, C:D.344, C:D.410, C:D.410

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

CL.10: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

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 C: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.226, C:Y.229, C:E.390, C:E.390, C:E.393

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

G88.12: 18 residues within 4Å: Chain A: F.166, R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, ZN.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.214, A:N.214, A:E.382, A:G.475, A:G.475, A:N.476, A:Y.509, A:Y.657 Salt bridges: A:R.167, A:H.510, A:K.656 G88.31: 18 residues within 4Å: Chain C: F.166, R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, Y.509, H.510, K.656, Y.657 Ligands: ZN.27, ZN.28 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.214, C:N.214, C:E.382, C:E.382, C:G.475, C:G.475, C:N.476, C:Y.509 Salt bridges: C:R.167, C:H.510, C:K.656

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.13: 4 residues within 4Å: Chain A: E.25, K.28, P.525, M.526 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.25 Hydrogen bonds: A:A.24 MPD.14: 5 residues within 4Å: Chain A: Y.328, L.398 Chain C: E.705, V.706 Ligands: ACT.35 No protein-ligand interaction detected (PLIP) MPD.15: 5 residues within 4Å: Chain A: R.562, D.587, F.590 Chain B: U.26, A.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.590, A:F.590 Hydrogen bonds: A:D.587, A:D.587 MPD.17: 6 residues within 4Å: Chain B: X.16, U.17, G.18, A.27, X.28, U.29 No protein-ligand interaction detected (PLIP) MPD.18: 3 residues within 4Å: Chain B: A.19, U.21, U.22 No protein-ligand interaction detected (PLIP) MPD.19: 4 residues within 4Å: Chain B: G.18, A.19, U.26, A.27 No protein-ligand interaction detected (PLIP) MPD.32: 4 residues within 4Å: Chain C: E.25, K.28, P.525, M.526 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.25 Hydrogen bonds: C:A.24 MPD.33: 5 residues within 4Å: Chain A: E.705, V.706 Chain C: Y.328, L.398 Ligands: ACT.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.66 MPD.34: 5 residues within 4Å: Chain C: R.562, D.587, F.590 Chain D: U.26, A.27 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.590, C:F.590 Hydrogen bonds: C:D.587 MPD.36: 6 residues within 4Å: Chain D: X.16, U.17, G.18, A.27, X.28, U.29 No protein-ligand interaction detected (PLIP) MPD.37: 3 residues within 4Å: Chain D: A.19, U.21, U.22 No protein-ligand interaction detected (PLIP) MPD.38: 4 residues within 4Å: Chain D: G.18, A.19, U.26, A.27 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.16: 4 residues within 4Å: Chain A: E.701 Chain C: E.394, N.395 Ligands: MPD.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.395 ACT.35: 4 residues within 4Å: Chain A: E.394, N.395 Chain C: E.701 Ligands: MPD.14 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:E.701 Hydrogen bonds: A:E.394, A:N.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ptacek, J. et al., Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nucleic Acids Res. (2020)

Release Date

2020-06-10

Peptides

Glutamate carboxypeptidase 2: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Glutamate carboxypeptidase 2

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