SMTL ID : 6ikz.1

UDP-glucose pyrophosphorylase from acinetobacter baumanii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: Q.105 Chain C: R.68 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.105 Salt bridges: C:R.68 SO4.2: 11 residues within 4Å: Chain A: T.55, E.63, S.100, V.101, R.102 Chain C: E.63, V.98, I.99, S.100 Ligands: SO4.11, SO4.12 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:E.63, C:V.98, C:S.100, C:S.100, A:E.63, A:S.100, A:R.102 Water bridges: A:R.102 Salt bridges: A:R.102 SO4.3: 6 residues within 4Å: Chain A: E.63, F.66, D.67, V.98 Chain C: R.102 Ligands: SO4.11 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:F.66, C:R.102 Salt bridges: C:R.102 SO4.4: 1 residues within 4Å: Chain A: R.149 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.149 SO4.8: 1 residues within 4Å: Ligands: UTP.7 No protein-ligand interaction detected (PLIP) SO4.9: 1 residues within 4Å: Chain B: R.149 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.149 SO4.10: 2 residues within 4Å: Chain A: R.68 Chain C: Q.105 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.105 Salt bridges: A:R.68 SO4.11: 11 residues within 4Å: Chain A: E.63, V.98, I.99, S.100 Chain C: T.55, E.63, S.100, V.101, R.102 Ligands: SO4.2, SO4.3 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:V.98, A:S.100, A:S.100, C:E.63, C:S.100, C:R.102 Water bridges: C:R.102 Salt bridges: C:R.102 SO4.12: 6 residues within 4Å: Chain A: R.102 Chain C: E.63, F.66, D.67, V.98 Ligands: SO4.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:F.66, A:R.102 Salt bridges: A:R.102 SO4.13: 1 residues within 4Å: Chain C: R.149 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.149 SO4.17: 1 residues within 4Å: Ligands: UTP.16 No protein-ligand interaction detected (PLIP) SO4.18: 1 residues within 4Å: Chain D: R.149 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.149

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.5: 5 residues within 4Å: Chain A: G.11, L.12, G.13, T.14, R.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.12, A:G.13, A:T.14, A:T.14, A:R.15 Salt bridges: A:R.15 PPV.14: 5 residues within 4Å: Chain C: G.11, L.12, G.13, T.14, R.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.12, C:G.13, C:T.14, C:T.14, C:R.15 Salt bridges: C:R.15

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: P.8, A.10, G.11, Q.103, G.108, L.109, A.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.10 GOL.15: 7 residues within 4Å: Chain C: P.8, A.10, G.11, Q.103, G.108, L.109, A.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.10

2 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)

UTP.7: 18 residues within 4Å: Chain A: K.79, K.81 Chain B: P.8, V.9, A.10, G.11, L.12, G.13, T.14, R.15, K.25, Q.103, P.106, L.107, G.108, L.109, D.131 Ligands: SO4.8 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.10, B:G.11, B:T.14, B:T.14, B:R.15, B:K.25, B:Q.103, B:Q.103, B:G.108, B:D.131 Salt bridges: B:R.15, A:K.79, A:K.81 UTP.16: 18 residues within 4Å: Chain C: K.79, K.81 Chain D: P.8, V.9, A.10, G.11, L.12, G.13, T.14, R.15, K.25, Q.103, P.106, L.107, G.108, L.109, D.131 Ligands: SO4.17 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:A.10, D:G.11, D:T.14, D:T.14, D:T.14, D:R.15, D:K.25, D:Q.103, D:Q.103, D:G.108, D:D.131 Salt bridges: D:R.15, C:K.79, C:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, L.W., UTP-bound UGPase from acinetobacter baumanii. To be published

Release Date

2019-10-16

Peptides

UTP--glucose-1-phosphate uridylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

UTP--glucose-1-phosphate uridylyltransferase

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