SMTL ID : 6k8d.1

UDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-tetramer

Ligands

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

UPG.1: 25 residues within 4Å: Chain A: P.8, V.9, A.10, G.11, E.26, Q.103, P.106, L.107, G.108, L.109, A.112, L.129, P.130, D.131, V.132, Y.171, G.172, E.193, V.206, V.207, Y.210, Q.232, T.234, D.257 Ligands: SO4.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.10, A:G.11, A:E.26, A:Q.103, A:Q.103, A:G.108, A:D.131, A:G.172, A:G.172, A:E.193, A:Q.232, A:D.257 UPG.5: 22 residues within 4Å: Chain B: P.8, V.9, A.10, G.11, K.25, E.26, Q.103, P.106, L.107, G.108, L.109, A.112, L.129, P.130, D.131, G.172, E.193, V.206, V.207, Y.210, T.234 Ligands: SO4.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.10, B:G.11, B:Q.103, B:Q.103, B:G.108, B:D.131, B:G.172, B:G.172, B:E.193, B:V.206, B:V.207 UPG.9: 21 residues within 4Å: Chain C: P.8, V.9, A.10, G.11, K.25, Q.103, P.106, L.107, G.108, L.109, A.112, L.129, P.130, D.131, Y.171, G.172, E.193, V.206, V.207, Y.210, T.234 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.10, C:G.11, C:K.25, C:K.25, C:Q.103, C:Q.103, C:G.108, C:G.172, C:G.172, C:V.207, C:Y.210, C:T.234 UPG.11: 21 residues within 4Å: Chain D: P.8, V.9, A.10, G.11, K.25, Q.103, P.106, L.107, G.108, L.109, A.112, L.129, P.130, D.131, Y.171, G.172, E.193, V.206, V.207, Y.210, Q.232 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:A.10, D:G.11, D:G.11, D:K.25, D:K.25, D:Q.103, D:Q.103, D:G.108, D:D.131, D:G.172, D:E.193, D:V.207, D:Q.232

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

SO4.2: 6 residues within 4Å: Chain A: G.11, L.12, G.13, T.14, K.25 Ligands: UPG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.11 SO4.3: 2 residues within 4Å: Chain A: Q.140, R.145 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.145 SO4.6: 2 residues within 4Å: Chain A: Q.105 Chain B: R.68 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.68 Hydrogen bonds: A:Q.105 SO4.7: 7 residues within 4Å: Chain B: G.11, L.12, G.13, T.14, R.15, K.25 Ligands: UPG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.12, B:T.14, B:R.15 SO4.10: 5 residues within 4Å: Chain A: K.79 Chain C: G.11, L.12, G.13, T.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:L.12, C:T.14, C:R.15 Salt bridges: A:K.79 SO4.12: 4 residues within 4Å: Chain D: L.12, G.13, T.14, R.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.14, D:R.15 SO4.13: 1 residues within 4Å: Chain D: K.117 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.117

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

EDO.4: 2 residues within 4Å: Chain A: H.111 Chain B: E.94 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain B: Q.140, R.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.140, B:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, L.W., UDP-glucose pyrophosphorylase with UPG from Acinetobacter Baumanii. To be published

Release Date

2020-06-17

Peptides

UTP--glucose-1-phosphate uridylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

UTP--glucose-1-phosphate uridylyltransferase

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