SMTL ID : 4r7p.1

Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-octamer

Ligands

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.1: 14 residues within 4Å: Chain A: L.131, N.132, G.133, G.134, Q.208, P.238, G.240, H.241, N.269, D.271, K.309, N.346, N.348, P.412 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.132, A:G.133, A:G.134, A:Q.208, A:Q.208, A:N.269, A:D.271 Salt bridges: A:H.241 pi-Stacking: A:H.241 UPG.43: 14 residues within 4Å: Chain E: L.131, N.132, G.133, G.134, Q.208, P.238, G.240, H.241, N.269, D.271, K.309, N.346, N.348, P.412 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.132, E:G.133, E:G.134, E:Q.208, E:Q.208, E:N.269, E:D.271, E:D.271 Salt bridges: E:H.241 pi-Stacking: E:H.241

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

SO4.2: 3 residues within 4Å: Chain A: E.45 Chain D: N.197, H.198 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: H.500 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: H.166 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: N.197, H.198 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: W.93, H.332 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: E.263, M.286 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: K.456, D.459 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: H.166, T.170 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: E.47, H.81 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain C: H.166, T.170 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: E.45, L.46 Chain C: H.198 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: E.465, D.525 Chain F: K.515 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain D: H.166, T.170 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: D.502, N.520 Chain E: N.520 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain D: L.461, R.462, F.464, E.465 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain E: E.45 Chain H: N.197, H.198 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain E: H.500 Ligand excluded by PLIP SO4.46: 1 residues within 4Å: Chain E: H.166 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain E: N.197, H.198 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain E: W.93, H.332 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain E: E.263, M.286 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain E: K.456, D.459 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain F: H.166, T.170 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain F: E.47, H.81 Ligand excluded by PLIP SO4.68: 2 residues within 4Å: Chain G: H.166, T.170 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain F: E.45, L.46 Chain G: H.198 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain B: K.515 Chain G: E.465, D.525 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain H: H.166, T.170 Ligand excluded by PLIP SO4.78: 3 residues within 4Å: Chain A: N.520 Chain H: D.502, N.520 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain H: L.461, R.462, F.464, E.465 Ligand excluded by PLIP

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

ACT.9: 4 residues within 4Å: Chain A: G.451, S.452, S.479 Chain D: L.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.452 ACT.29: 1 residues within 4Å: Chain C: H.500 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.500 ACT.38: 2 residues within 4Å: Chain B: G.501 Chain D: H.500 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.500 ACT.39: 2 residues within 4Å: Chain D: E.472, E.513 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.513 Salt bridges: D:K.491 ACT.51: 4 residues within 4Å: Chain E: G.451, S.452, S.479 Chain H: L.524 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.452 ACT.71: 1 residues within 4Å: Chain G: H.500 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:H.500 ACT.80: 2 residues within 4Å: Chain F: G.501 Chain H: H.500 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:H.500 ACT.81: 2 residues within 4Å: Chain H: E.472, E.513 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.513 Salt bridges: H:K.491

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

EDO.10: 3 residues within 4Å: Chain A: K.491, E.513 Chain E: K.337 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: N.184, D.188 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Q.105, H.284, P.289 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: R.43 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.472, K.491, E.513 Chain F: K.337 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: C.141, K.142, Q.458 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain B: D.117 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: D.525 Chain G: K.515 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.462, R.463, T.483 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain B: K.449 Chain C: H.526 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain D: K.456, D.459 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain A: K.337 Chain E: K.491, E.513 Ligand excluded by PLIP EDO.53: 2 residues within 4Å: Chain E: N.184, D.188 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain E: Q.105, H.284, P.289 Ligand excluded by PLIP EDO.55: 1 residues within 4Å: Chain E: R.43 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain B: K.337 Chain F: E.472, K.491, E.513 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain F: C.141, K.142, Q.458 Ligand excluded by PLIP EDO.62: 1 residues within 4Å: Chain F: D.117 Ligand excluded by PLIP EDO.63: 2 residues within 4Å: Chain C: K.515 Chain F: D.525 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain F: R.462, R.463, T.483 Ligand excluded by PLIP EDO.72: 2 residues within 4Å: Chain F: K.449 Chain G: H.526 Ligand excluded by PLIP EDO.82: 2 residues within 4Å: Chain H: K.456, D.459 Ligand excluded by PLIP

22 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.14: 1 residues within 4Å: Chain A: E.65 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:E.65, H2O.2 ZN.15: 2 residues within 4Å: Chain A: C.141, Q.458 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.141, H2O.2 ZN.23: 1 residues within 4Å: Chain B: D.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.188, B:D.188 ZN.24: 2 residues within 4Å: Chain B: N.197, H.198 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.198 ZN.25: 3 residues within 4Å: Chain B: H.475 Chain F: H.475 Ligands: ZN.67 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Metal complexes: B:H.475, F:H.475 ZN.31: 2 residues within 4Å: Chain C: G.240, H.241 No protein-ligand interaction detected (PLIP) ZN.32: 2 residues within 4Å: Chain C: E.165, C.199 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.165, C:E.165, C:C.199 ZN.33: 3 residues within 4Å: Chain C: K.456, D.459, R.462 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.459, C:D.459, H2O.4 ZN.34: 3 residues within 4Å: Chain C: Q.105, I.110, H.284 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.284, C:H.284 ZN.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.42: 2 residues within 4Å: Chain D: E.165, C.199 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.165, D:E.165, D:C.199 ZN.56: 1 residues within 4Å: Chain E: E.65 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.65, E:E.65, H2O.6 ZN.57: 2 residues within 4Å: Chain E: C.141, Q.458 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.141, H2O.6 ZN.65: 1 residues within 4Å: Chain F: D.188 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.188, F:D.188 ZN.66: 2 residues within 4Å: Chain F: N.197, H.198 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.198 ZN.67: 3 residues within 4Å: Chain B: H.475 Chain F: H.475 Ligands: ZN.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Metal complexes: B:H.475, F:H.475 ZN.73: 2 residues within 4Å: Chain G: G.240, H.241 No protein-ligand interaction detected (PLIP) ZN.74: 2 residues within 4Å: Chain G: E.165, C.199 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.165, G:E.165, G:C.199 ZN.75: 3 residues within 4Å: Chain G: K.456, D.459, R.462 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.459, G:D.459, H2O.8 ZN.76: 3 residues within 4Å: Chain G: Q.105, I.110, H.284 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.284, G:H.284 ZN.83: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.84: 2 residues within 4Å: Chain H: E.165, C.199 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.165, H:E.165, H:C.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuhring, J.I. et al., A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism. Sci Rep

Release Date

2015-04-22

Peptides

UTP--glucose-1-phosphate uridylyltransferase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

UTP--glucose-1-phosphate uridylyltransferase