SMTL ID : 5in3.1

Crystal structure of glucose-1-phosphate bound nucleotidylated human galactose-1-phosphate uridylyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: L.59, Q.60, E.224, H.323, H.341, H.343 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.224, A:E.224, A:H.323, A:H.341, A:H.343 ZN.19: 6 residues within 4Å: Chain B: L.59, Q.60, E.224, H.323, H.341, H.343 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:E.224, B:H.323, B:H.341, B:H.343

2 x H2U: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE(Non-covalent)

H2U.2: 16 residues within 4Å: Chain A: P.95, L.96, R.102, A.103, F.117, N.119, D.120, F.121, V.150, N.195, C.202, S.203, N.204, H.208, Q.210 Ligands: G1P.34 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.95 Hydrogen bonds: A:A.103, A:N.119, A:D.120, A:D.120, A:Q.210, A:Q.210 Water bridges: A:N.195, A:N.195, A:N.195, A:N.204 Salt bridges: A:H.208 pi-Stacking: A:F.121 H2U.20: 16 residues within 4Å: Chain B: P.95, L.96, R.102, A.103, F.117, N.119, D.120, F.121, V.150, N.195, C.202, S.203, N.204, H.208, Q.210 Ligands: G1P.18 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.95 Hydrogen bonds: B:A.103, B:N.119, B:N.119, B:D.120, B:D.120, B:Q.210 Water bridges: B:N.195, B:N.195, B:S.203 Salt bridges: B:H.208 pi-Stacking: B:F.121

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

EDO.3: 7 residues within 4Å: Chain A: R.281, H.282, V.283, R.284, E.288, N.336 Ligands: EDO.9 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: S.130, S.143, R.145 Ligands: EDO.10 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: R.70, P.272, L.349, K.356, Q.368, R.369, D.370, L.371 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.284, R.285, A.331, G.332, W.335 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Q.140, K.142 Chain B: Y.56, W.63 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: E.237, P.238, M.241, H.282 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: H.282, N.336 Ligands: EDO.3, EDO.8 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: S.130, P.131, A.141, K.142, S.143 Ligands: EDO.4 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: M.241, S.244, R.245, L.248, R.280 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: D.174, A.177, S.178, E.181, P.287, R.294 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: E.378, R.381, A.382 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: D.112, H.154, P.155, W.156 Ligands: EDO.17 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain A: F.153, L.161, W.176, E.194, C.209, M.301, L.305, Y.318, M.320, W.322, Y.344 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: R.245, Q.246, L.249 Chain B: H.136 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: R.89, W.156 Ligands: EDO.14 Ligand excluded by PLIP EDO.21: 10 residues within 4Å: Chain B: D.118, N.119, P.122, L.124, Q.125, P.126, G.146, V.147, C.148, K.149 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: P.188, L.217, P.326, T.327, G.328, S.329, W.335 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: D.112, H.154, P.155, W.156, E.168 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain B: H.154, W.156, V.159, L.163, M.164, S.165, E.168 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: F.139 Chain B: R.250, E.252, R.253, F.267 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain B: R.70, P.272, L.349, K.356, Q.368, R.369, D.370, L.371 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: S.130, S.143, R.145 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: E.237, P.238, M.241, E.242, R.245 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: H.90, P.98, G.99, Q.110 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain B: R.281, H.282, V.283, R.284, R.285, E.288, N.336 Ligands: EDO.32 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: P.88, R.89, D.158 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: H.282, N.336 Ligands: EDO.30 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain B: R.89, W.156 Ligand excluded by PLIP

2 x G1P: 1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G1P.18: 14 residues within 4Å: Chain A: K.356, F.357, V.359, G.360, Y.361, E.362, Q.368 Chain B: F.193, N.195, G.201, C.202, Q.210, W.212 Ligands: H2U.20 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.356, A:F.357, A:F.357, A:Y.361, B:N.195, B:Q.210 Water bridges: A:R.70, A:Q.368, B:N.119, B:Q.210 G1P.34: 14 residues within 4Å: Chain A: F.193, N.195, G.201, C.202, Q.210, W.212 Chain B: K.356, F.357, V.359, G.360, Y.361, E.362, Q.368 Ligands: H2U.2 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.356, B:F.357, B:F.357, B:Y.361, B:E.362, A:N.195, A:G.201, A:Q.210 Water bridges: B:R.70, B:R.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCorvie, T.J. et al., Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase. Hum.Mol.Genet. (2016)

Release Date

2016-03-30

Peptides

Galactose-1-phosphate uridylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Galactose-1-phosphate uridylyltransferase