SMTL ID : 5l4z.1

Crystal structure of enzyme in purine metabolism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

52 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: K.381, R.475, Y.476 Chain C: A.133, Y.134, R.163, R.475 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: D.271, Y.272, V.307, D.308, G.329, K.330, L.331 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: T.116, E.393, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: D.73, H.228, Y.229, K.234, S.270, Y.274 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: R.58, K.380, R.386, D.478 Chain C: D.132, Y.134, N.136 Ligands: GOL.13 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: D.276, T.280, P.297, W.298, Q.299 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: V.54, V.56, Y.490, Y.494, L.495, F.496, R.497 Ligands: GOL.12 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: N.136, L.137, R.153, K.159, R.465 Chain C: K.363 Ligands: GOL.39 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: Y.170, F.217, Q.218, R.221 Ligand excluded by PLIP GOL.11: 1 residues within 4Å: Chain A: F.210 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: R.53, V.54, F.55, V.56 Chain C: P.504 Ligands: GOL.8 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: K.64, K.363, R.386 Ligands: GOL.6, GOL.35 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: K.381, R.475, Y.476 Chain D: A.133, Y.134, R.163, R.475 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: D.271, Y.272, V.307, D.308, G.329, K.330, L.331 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain B: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: T.116, E.393, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: D.73, H.228, Y.229, K.234, S.270, Y.274 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain B: R.58, K.380, R.386, D.478 Chain D: D.132, Y.134, N.136 Ligands: GOL.26 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: D.276, T.280, P.297, W.298, Q.299 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: V.54, V.56, Y.490, Y.494, L.495, F.496, R.497 Ligands: GOL.25 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: N.136, L.137, R.153, K.159, R.465 Chain D: K.363 Ligands: GOL.52 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain B: Y.170, F.217, Q.218, R.221 Ligand excluded by PLIP GOL.24: 1 residues within 4Å: Chain B: F.210 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: R.53, V.54, F.55, V.56 Chain D: P.504 Ligands: GOL.21 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: K.64, K.363, R.386 Ligands: GOL.19, GOL.48 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain A: A.133, Y.134, R.163, R.475 Chain C: K.381, R.475, Y.476 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: D.271, Y.272, V.307, D.308, G.329, K.330, L.331 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: T.116, E.393, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: D.73, H.228, Y.229, K.234, S.270, Y.274 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain A: D.132, Y.134, N.136 Chain C: R.58, K.380, R.386, D.478 Ligands: GOL.39 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain C: D.276, T.280, P.297, W.298, Q.299 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain C: V.54, V.56, Y.490, Y.494, L.495, F.496, R.497 Ligands: GOL.38 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain A: K.363 Chain C: N.136, L.137, R.153, K.159, R.465 Ligands: GOL.13 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain C: Y.170, F.217, Q.218, R.221 Ligand excluded by PLIP GOL.37: 1 residues within 4Å: Chain C: F.210 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain A: P.504 Chain C: R.53, V.54, F.55, V.56 Ligands: GOL.34 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain C: K.64, K.363, R.386 Ligands: GOL.9, GOL.32 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain B: A.133, Y.134, R.163, R.475 Chain D: K.381, R.475, Y.476 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: D.271, Y.272, V.307, D.308, G.329, K.330, L.331 Ligand excluded by PLIP GOL.42: 8 residues within 4Å: Chain D: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain D: T.116, E.393, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: D.73, H.228, Y.229, K.234, S.270, Y.274 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain B: D.132, Y.134, N.136 Chain D: R.58, K.380, R.386, D.478 Ligands: GOL.52 Ligand excluded by PLIP GOL.46: 5 residues within 4Å: Chain D: D.276, T.280, P.297, W.298, Q.299 Ligand excluded by PLIP GOL.47: 8 residues within 4Å: Chain D: V.54, V.56, Y.490, Y.494, L.495, F.496, R.497 Ligands: GOL.51 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain B: K.363 Chain D: N.136, L.137, R.153, K.159, R.465 Ligands: GOL.26 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain D: Y.170, F.217, Q.218, R.221 Ligand excluded by PLIP GOL.50: 1 residues within 4Å: Chain D: F.210 Ligand excluded by PLIP GOL.51: 6 residues within 4Å: Chain B: P.504 Chain D: R.53, V.54, F.55, V.56 Ligands: GOL.47 Ligand excluded by PLIP GOL.52: 5 residues within 4Å: Chain D: K.64, K.363, R.386 Ligands: GOL.22, GOL.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hnizda, A. et al., Oligomeric interface modulation causes misregulation of purine 5 -nucleotidase in relapsed leukemia. Bmc Biol. (2016)

Release Date

2016-09-21

Peptides

Cytosolic purine 5'-nucleotidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cytosolic purine 5'-nucleotidase