SMTL ID : 3zy5.1

Crystal structure of POFUT1 in complex with GDP-fucose (crystal-form-I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: C.98, W.99, S.172, S.173 Chain B: T.100, R.102 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.99, A:S.173 Water bridges: A:S.172, A:S.172 Salt bridges: B:R.102 SO4.2: 5 residues within 4Å: Chain A: H.115, S.116, K.117, E.118, F.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.116, A:K.117 Water bridges: A:E.111, A:H.115, A:F.133, A:F.133 SO4.3: 6 residues within 4Å: Chain A: Q.150, M.151, G.152, S.153, R.154, K.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.152, A:S.153, A:R.154, A:K.155 Salt bridges: A:R.154 SO4.4: 3 residues within 4Å: Chain A: Q.64, V.65, G.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.65, A:G.66 Water bridges: A:T.67, A:T.67 SO4.7: 6 residues within 4Å: Chain A: T.100, R.102 Chain B: C.98, W.99, S.172, S.173 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.99, B:S.173 Water bridges: B:S.172, B:S.172 Salt bridges: A:R.102 SO4.8: 5 residues within 4Å: Chain B: H.115, S.116, K.117, E.118, F.133 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.116, B:K.117 Water bridges: B:H.115, B:H.115, B:F.133, B:F.133 SO4.9: 6 residues within 4Å: Chain B: Q.150, M.151, G.152, S.153, R.154, K.155 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.152, B:S.153, B:R.154, B:K.155 Salt bridges: B:R.154 SO4.10: 3 residues within 4Å: Chain B: Q.64, V.65, G.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.65, B:G.66 Water bridges: B:T.67, B:T.67

2 x GFB: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE(Non-covalent)

GFB.5: 18 residues within 4Å: Chain A: R.19, F.20, G.21, N.22, H.217, R.219, W.224, F.240, A.286, S.287, D.288, D.313, M.315, S.334, T.335, F.336 Chain B: A.110, P.112 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.19, A:F.20, A:G.21, A:N.22, A:N.22, A:D.313, A:T.335, A:T.335, A:T.335, A:F.336, B:A.110 Water bridges: A:G.18, A:R.19, A:R.219 Salt bridges: A:R.219, A:R.219, A:R.219, A:D.313 pi-Stacking: A:F.336 GFB.11: 18 residues within 4Å: Chain A: A.110, P.112 Chain B: R.19, F.20, G.21, N.22, H.217, R.219, W.224, F.240, A.286, S.287, D.288, D.313, M.315, S.334, T.335, F.336 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.19, B:F.20, B:G.21, B:N.22, B:N.22, B:D.313, B:T.335, B:T.335, B:F.336, A:A.110 Water bridges: B:G.18, B:R.19, B:R.219 Salt bridges: B:R.219, B:R.219, B:R.219, B:D.313 pi-Stacking: B:F.336

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.6: 13 residues within 4Å: Chain A: W.99, T.100, P.101, Y.138, G.140, D.141 Chain B: W.99, G.144, F.146, D.147, P.177, F.178, K.181 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:F.178, B:F.178, B:K.181, B:K.181, A:W.99, A:T.100, A:G.140, A:G.140 Salt bridges: B:D.147 Water bridges: A:D.141 BTB.12: 13 residues within 4Å: Chain A: W.99, G.144, F.146, D.147, P.177, F.178, K.181 Chain B: W.99, T.100, P.101, Y.138, G.140, D.141 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:F.178, A:F.178, A:K.181, A:K.181, B:W.99, B:G.140, B:G.140 Salt bridges: A:D.147 Water bridges: B:D.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lira-Navarrete, E. et al., Structural Insights Into the Mechanism of Protein O-Fucosylation. Plos One (2011)

Release Date

2011-09-14

Peptides

PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1

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