SMTL ID : 3vp1.1

Crystal structure of human glutaminase in complex with L-glutamate and BPTES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x 04A: N,N'-[sulfanediylbis(ethane-2,1-diyl-1,3,4-thiadiazole-5,2-diyl)]bis(2-phenylacetamide)(Non-covalent)

04A.1: 12 residues within 4Å: Chain A: R.99, F.100, L.103, F.104, L.105, N.106, E.107, Y.176 Chain B: K.102, F.104 Chain D: R.99 Ligands: 04A.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.100, A:L.103, A:E.107, A:Y.176, B:F.104 Hydrogen bonds: A:L.105, A:L.105, A:Y.176 Water bridges: A:D.109 04A.5: 12 residues within 4Å: Chain A: K.102, F.104 Chain B: R.99, F.100, L.103, F.104, L.105, N.106, E.107, Y.176 Chain C: R.99 Ligands: 04A.1 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.100, B:L.103, B:E.107, B:Y.176, A:F.104 Hydrogen bonds: B:L.105, B:L.105 04A.9: 12 residues within 4Å: Chain B: R.99 Chain C: R.99, F.100, L.103, F.104, L.105, N.106, E.107, Y.176 Chain D: K.102, F.104 Ligands: 04A.13 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.100, C:L.103, C:E.107, C:Y.176, D:F.104 Hydrogen bonds: C:L.105, C:L.105, C:Y.176 Water bridges: C:D.109 04A.13: 12 residues within 4Å: Chain A: R.99 Chain C: K.102, F.104 Chain D: R.99, F.100, L.103, F.104, L.105, N.106, E.107, Y.176 Ligands: 04A.9 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.100, D:L.103, D:E.107, D:Y.176, C:F.104 Hydrogen bonds: D:L.105, D:L.105

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 10 residues within 4Å: Chain A: Y.31, Q.67, S.68, N.117, E.163, N.170, Y.196, Y.248, G.265, V.266 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Q.67, A:S.68, A:S.68, A:N.117, A:N.170, A:V.266, E.2, E.2 Water bridges: A:Y.248 Salt bridges: A:K.71, A:K.71 GLU.6: 10 residues within 4Å: Chain B: Y.31, Q.67, S.68, N.117, E.163, N.170, Y.196, Y.248, G.265, V.266 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:Y.31, B:Q.67, B:S.68, B:S.68, B:N.117, B:N.170, B:Y.196, B:Y.248, B:V.266, E.6, E.6 Salt bridges: B:K.71, B:K.71 GLU.10: 10 residues within 4Å: Chain C: Y.31, Q.67, S.68, N.117, E.163, N.170, Y.196, Y.248, G.265, V.266 11 PLIP interactions: 9 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:Q.67, C:S.68, C:S.68, C:N.117, C:N.170, C:V.266, E.10, E.10 Water bridges: C:Y.248 Salt bridges: C:K.71, C:K.71 GLU.14: 10 residues within 4Å: Chain D: Y.31, Q.67, S.68, N.117, E.163, N.170, Y.196, Y.248, G.265, V.266 13 PLIP interactions: 2 Ligand-Ligand interactions, 11 interactions with chain D Hydrogen bonds: E.14, E.14, D:Y.31, D:Q.67, D:S.68, D:S.68, D:N.117, D:N.170, D:Y.196, D:Y.248, D:V.266 Salt bridges: D:K.71, D:K.71

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: F.155, N.157, A.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.157, A:A.158 SO4.4: 4 residues within 4Å: Chain A: Y.176, K.180 Chain B: K.102, R.169 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.102, B:R.169, A:K.180 Hydrogen bonds: A:Y.176 SO4.7: 3 residues within 4Å: Chain B: F.155, N.157, A.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.157, B:A.158 SO4.8: 4 residues within 4Å: Chain A: K.102, R.169 Chain B: Y.176, K.180 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.176, B:Y.176 Salt bridges: B:K.180, A:K.102, A:R.169 SO4.11: 3 residues within 4Å: Chain C: F.155, N.157, A.158 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.157, C:A.158 SO4.12: 4 residues within 4Å: Chain C: Y.176, K.180 Chain D: K.102, R.169 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.102, D:R.169, C:K.180 Hydrogen bonds: C:Y.176 SO4.15: 3 residues within 4Å: Chain D: F.155, N.157, A.158 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.157, D:A.158 SO4.16: 4 residues within 4Å: Chain C: K.102, R.169 Chain D: Y.176, K.180 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.176, D:Y.176 Salt bridges: D:K.180, C:K.102, C:R.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thangavelu, K. et al., Structural basis for the allosteric inhibitory mechanism of human kidney-type glutaminase (KGA) and its regulation by Raf-Mek-Erk signaling in cancer cell metabolism. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-06-13

Peptides

Glutaminase kidney isoform, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glutaminase kidney isoform, mitochondrial

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