SMTL ID : 8szj.1

Human glutaminase C (Y466W) with L-Gln and Pi, filamentous form

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: K.320, R.387 Chain C: Y.394, K.398 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.394, C:Y.394 Salt bridges: C:K.398, A:K.320, A:R.387 PO4.3: 4 residues within 4Å: Chain B: K.320, R.387 Chain D: Y.394, K.398 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Salt bridges: B:K.320, B:R.387, D:K.398 PO4.5: 4 residues within 4Å: Chain A: Y.394, K.398 Chain C: K.320, R.387 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.394, A:Y.394 Salt bridges: A:K.398, C:K.320, C:R.387 PO4.7: 4 residues within 4Å: Chain B: Y.394, K.398 Chain D: K.320, R.387 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:K.320, D:R.387, B:K.398 PO4.9: 5 residues within 4Å: Chain E: N.319, K.320, R.387 Chain G: Y.394, K.398 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain G Salt bridges: E:K.320, E:R.387, G:K.398 Hydrogen bonds: G:Y.394 PO4.11: 4 residues within 4Å: Chain F: K.320, R.387 Chain H: Y.394, K.398 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H Salt bridges: F:K.320, F:R.387, H:K.398 PO4.13: 3 residues within 4Å: Chain E: K.398 Chain G: K.320, R.387 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:Y.394 Salt bridges: E:K.398, G:K.320, G:R.387 PO4.15: 4 residues within 4Å: Chain F: Y.394, K.398 Chain H: K.320, R.387 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F Salt bridges: H:K.320, H:R.387, F:K.398 PO4.17: 4 residues within 4Å: Chain I: K.320, R.387 Chain K: Y.394, K.398 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain K Salt bridges: I:K.320, I:R.387, K:K.398 Hydrogen bonds: K:Y.394, K:Y.394 PO4.19: 4 residues within 4Å: Chain J: K.320, R.387 Chain L: Y.394, K.398 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L Salt bridges: J:K.320, J:R.387, L:K.398 PO4.21: 4 residues within 4Å: Chain I: Y.394, K.398 Chain K: K.320, R.387 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain I Salt bridges: K:R.387, I:K.398 Hydrogen bonds: I:Y.394, I:Y.394 PO4.23: 4 residues within 4Å: Chain J: Y.394, K.398 Chain L: K.320, R.387 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L Salt bridges: J:K.398, L:K.320, L:R.387

12 x GLN: GLUTAMINE(Non-covalent)

GLN.2: 12 residues within 4Å: Chain A: Y.249, I.250, Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Q.285, A:V.484 Hydrogen bonds: A:S.286, A:K.289, A:N.335, A:E.381, A:E.381, A:N.388, A:Y.414, A:Y.414, A:V.484, Q.2, Q.2 GLN.4: 10 residues within 4Å: Chain B: Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Q.285, B:V.484 Hydrogen bonds: B:S.286, B:K.289, B:N.335, B:E.381, B:N.388, B:Y.414, B:V.484, Q.4 GLN.6: 12 residues within 4Å: Chain C: Y.249, I.250, Q.285, S.286, K.289, F.318, N.319, N.335, E.381, N.388, Y.414, V.484 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:V.484 Hydrogen bonds: C:Y.249, C:Y.249, C:K.289, C:N.319, C:N.335, C:E.381, C:N.388, C:Y.414 GLN.8: 10 residues within 4Å: Chain D: Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 11 PLIP interactions: 9 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Q.285, D:V.484 Hydrogen bonds: D:Q.285, D:S.286, D:K.289, D:N.335, D:N.388, D:V.484, Q.8, Q.8 Salt bridges: D:K.289 GLN.10: 12 residues within 4Å: Chain E: Y.249, I.250, Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 11 PLIP interactions: 9 interactions with chain E, 2 Ligand-Ligand interactions Hydrophobic interactions: E:V.484 Hydrogen bonds: E:Y.249, E:S.286, E:K.289, E:N.335, E:E.381, E:N.388, E:Y.414, E:V.484, Q.10, Q.10 GLN.12: 10 residues within 4Å: Chain F: Y.249, Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, V.484 8 PLIP interactions: 7 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: F:S.286, F:K.289, F:N.335, F:E.381, F:N.388, F:N.388, F:V.484, Q.12 GLN.14: 11 residues within 4Å: Chain G: Y.249, I.250, Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, V.484 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:V.484 Hydrogen bonds: G:Y.249, G:Y.249, G:S.286, G:K.289, G:N.335, G:N.388, G:Y.414 GLN.16: 10 residues within 4Å: Chain H: Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 10 PLIP interactions: 9 interactions with chain H, 1 Ligand-Ligand interactions Hydrophobic interactions: H:V.484 Hydrogen bonds: H:Q.285, H:S.286, H:K.289, H:N.335, H:N.388, H:Y.414, H:V.484, Q.16 Salt bridges: H:K.289 GLN.18: 12 residues within 4Å: Chain I: Y.249, I.250, Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, C.418, V.484 11 PLIP interactions: 9 interactions with chain I, 2 Ligand-Ligand interactions Hydrophobic interactions: I:Q.285, I:V.484 Hydrogen bonds: I:Y.249, I:S.286, I:K.289, I:N.335, I:E.381, I:N.388, I:Y.414, Q.18, Q.18 GLN.20: 9 residues within 4Å: Chain J: Q.285, S.286, K.289, N.335, E.381, N.388, Y.414, C.418, V.484 11 PLIP interactions: 10 interactions with chain J, 1 Ligand-Ligand interactions Hydrophobic interactions: J:Q.285, J:V.484 Hydrogen bonds: J:S.286, J:K.289, J:N.335, J:E.381, J:N.388, J:Y.414, J:V.484, Q.20 Salt bridges: J:K.289 GLN.22: 12 residues within 4Å: Chain K: Y.249, I.250, Q.285, S.286, K.289, F.318, N.319, N.335, E.381, N.388, Y.414, V.484 9 PLIP interactions: 9 interactions with chain K, Hydrogen bonds: K:Y.249, K:Y.249, K:S.286, K:K.289, K:N.319, K:N.335, K:E.381, K:N.388, K:Y.414 GLN.24: 9 residues within 4Å: Chain L: Q.285, S.286, K.289, F.318, N.335, E.381, N.388, Y.414, V.484 10 PLIP interactions: 9 interactions with chain L, 1 Ligand-Ligand interactions Hydrophobic interactions: L:V.484 Hydrogen bonds: L:Q.285, L:S.286, L:K.289, L:N.335, L:N.388, L:Y.414, L:V.484, Q.24 Salt bridges: L:K.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, S. et al., Filament formation drives catalysis by glutaminase enzymes important in cancer progression. Nat Commun (2024)

Release Date

2024-03-13

Peptides

Glutaminase kidney isoform, mitochondrial: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

G
I

H
K

I
F

J
H

K
J

L
L

Glutaminase kidney isoform, mitochondrial