SMTL ID : 7bfz.1

X-ray structure of human prostate-specific membrane antigen(PSMA) in complex with a inhibitor Glu-490

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

4 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.36, Q.52, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.52 NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.608, A:Q.608, A:Q.608 NAG-NAG-BMA.19: 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-BMA.23: 5 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.608, B:Q.608, B:Q.608

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.2: 11 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 Ligands: EDO.31 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:H.69 NAG-NAG-BMA-MAN-MAN.20: 11 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 Ligands: EDO.13 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:H.69

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.4: 5 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97, L.100 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.84, A:L.100 NAG-NAG-BMA-FUC.22: 5 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97, L.100 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.84, B:L.100

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.7, TKZ.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.7: 6 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.6 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.24: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.25, TKZ.36 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.30 ZN.25: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.24 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.30

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP

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

NAG.10: 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.11: 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.28: 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.29: 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

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

EDO.12: 4 residues within 4Å: Chain A: N.14, M.15, F.542, E.543 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.15, A:E.543 Water bridges: A:N.14, A:K.16 EDO.13: 4 residues within 4Å: Chain A: Q.54, E.66, L.67 Ligands: NAG-NAG-BMA-MAN-MAN.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.54, A:L.67, A:L.67 EDO.15: 6 residues within 4Å: Chain A: P.461, E.462, P.467, R.468, I.469 Ligands: TKZ.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.462, A:R.468, A:I.469 EDO.30: 4 residues within 4Å: Chain B: N.14, M.15, F.542, E.543 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.15, B:E.543 Water bridges: B:N.14, B:K.16 EDO.31: 4 residues within 4Å: Chain B: Q.54, E.66, L.67 Ligands: NAG-NAG-BMA-MAN-MAN.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.54, B:L.67, B:L.67 EDO.33: 6 residues within 4Å: Chain B: P.461, E.462, P.467, R.468, I.469 Ligands: TKZ.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.462, B:R.468, B:I.469

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

PEG.14: 5 residues within 4Å: Chain A: W.391, L.398 Chain B: E.701, E.705, V.706 No protein-ligand interaction detected (PLIP) PEG.32: 5 residues within 4Å: Chain A: E.701, E.705, V.706 Chain B: W.391, L.398 No protein-ligand interaction detected (PLIP)

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

NA.16: 4 residues within 4Å: Chain A: Y.108, Y.199, T.515, E.517 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.199, A:T.515, A:E.517 NA.17: 3 residues within 4Å: Chain A: E.443, K.457, Y.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.443, A:E.443 NA.34: 4 residues within 4Å: Chain B: Y.108, Y.199, T.515, E.517 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.199, B:Y.199, B:T.515 NA.35: 3 residues within 4Å: Chain B: E.443, K.457, Y.529 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.443, B:E.443

2 x TKZ: (((S)-1-carboxy-5-((E)-2-cyano-3-(5-(1-(3-methoxy-3-oxopropyl)-1,2,3,4-tetrahydroquinolin-6-yl)thiophen-2-yl)acrylamido)pentyl)carbamoyl)-L-glutamic acid(Non-covalent)

TKZ.18: 27 residues within 4Å: Chain A: G.163, K.164, V.165, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, S.470, K.471, G.475, N.476, R.491, R.493, F.503, G.505, Y.509, H.510, N.655, K.656, Y.657, A.658 Ligands: ZN.6, EDO.15 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.385, A:F.503, A:F.503, A:Y.509, A:Y.657, A:Y.657 Hydrogen bonds: A:N.214, A:G.475, A:G.475, A:N.476, A:G.505, A:Y.657 Water bridges: A:R.167, A:K.170, A:N.214, A:D.344, A:E.414, A:R.468, A:R.491, A:S.504, A:K.656 Salt bridges: A:R.167, A:K.471, A:R.491, A:R.493, A:H.510, A:K.656 pi-Stacking: A:F.503 TKZ.36: 27 residues within 4Å: Chain B: G.163, K.164, V.165, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, S.470, K.471, G.475, N.476, R.491, R.493, F.503, G.505, Y.509, H.510, N.655, K.656, Y.657, A.658 Ligands: ZN.24, EDO.33 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.385, B:F.503, B:F.503, B:Y.509, B:Y.657, B:Y.657 Hydrogen bonds: B:N.214, B:G.475, B:G.475, B:N.476, B:G.505, B:Y.657 Water bridges: B:R.167, B:K.170, B:N.214, B:D.344, B:E.414, B:R.468, B:R.491, B:S.504, B:K.656 Salt bridges: B:R.167, B:K.471, B:R.491, B:R.493, B:H.510, B:K.656 pi-Stacking: B:F.503

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., A prostate-specific membrane antigen activated molecular rotor for real-time fluorescence imaging. Nat Commun (2021)

Release Date

2021-08-18

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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