SMTL ID : 1hm9.1 (1 other biounit)

CRYSTAL STRUCTURE OF S.PNEUMONIAE N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, GLMU, BOUND TO ACETYL COENZYME A AND UDP-N-ACETYLGLUCOSAMINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: K.31, D.111, N.236 Ligands: UD1.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.111, H2O.3, H2O.3 CA.2: 2 residues within 4Å: Chain A: R.24 Ligands: UD1.6 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: D.407, D.425 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.407, A:D.425, A:D.425, H2O.9 CA.4: 5 residues within 4Å: Chain A: N.414 Chain B: N.414 Chain C: N.414 Ligands: CA.10, CA.16 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain B: K.31, D.111, N.236 Ligands: UD1.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.111, H2O.16, H2O.17 CA.8: 2 residues within 4Å: Chain B: R.24 Ligands: UD1.12 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: D.407, D.425 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.407, B:D.425, B:D.425, H2O.22 CA.10: 5 residues within 4Å: Chain A: N.414 Chain B: N.414 Chain C: N.414 Ligands: CA.4, CA.16 No protein-ligand interaction detected (PLIP) CA.13: 4 residues within 4Å: Chain C: K.31, D.111, N.236 Ligands: UD1.18 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.111, H2O.30, H2O.30 CA.14: 2 residues within 4Å: Chain C: R.24 Ligands: UD1.18 No protein-ligand interaction detected (PLIP) CA.15: 2 residues within 4Å: Chain C: D.407, D.425 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.407, C:D.425, C:D.425, H2O.36 CA.16: 5 residues within 4Å: Chain A: N.414 Chain B: N.414 Chain C: N.414 Ligands: CA.4, CA.10 No protein-ligand interaction detected (PLIP)

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.5: 21 residues within 4Å: Chain A: Y.374, I.391, T.392, V.393, N.394, Y.395, I.418 Chain B: H.371, G.387, A.388, F.410, G.412, S.413, G.430, A.431, I.446, R.448, R.450 Chain C: I.452, K.454, Y.457 21 PLIP interactions: 5 interactions with chain A, 13 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:Y.374, A:I.391, A:V.393, B:A.388, B:F.410, B:I.446 Hydrogen bonds: A:Y.395, B:A.388, B:S.413, B:A.431, B:R.448, B:R.448, B:R.448, B:R.450, C:Y.457, C:Y.457 Water bridges: A:N.394, B:R.448, B:R.448 pi-Cation interactions: B:R.450 Salt bridges: C:K.454 ACO.11: 21 residues within 4Å: Chain A: I.452, K.454, Y.457 Chain B: Y.374, I.391, T.392, V.393, N.394, Y.395, I.418 Chain C: H.371, G.387, A.388, F.410, G.412, S.413, G.430, A.431, I.446, R.448, R.450 21 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, 13 interactions with chain C Hydrophobic interactions: B:Y.374, B:I.391, B:V.393, C:A.388, C:F.410, C:I.446 Hydrogen bonds: B:Y.395, A:Y.457, A:Y.457, C:A.388, C:S.413, C:A.431, C:R.448, C:R.448, C:R.448, C:R.450 Water bridges: B:N.394, C:R.448, C:R.448 Salt bridges: A:K.454 pi-Cation interactions: C:R.450 ACO.17: 21 residues within 4Å: Chain A: H.371, G.387, A.388, F.410, G.412, S.413, G.430, A.431, I.446, R.448, R.450 Chain B: I.452, K.454, Y.457 Chain C: Y.374, I.391, T.392, V.393, N.394, Y.395, I.418 21 PLIP interactions: 13 interactions with chain A, 5 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:A.388, A:F.410, A:I.446, C:Y.374, C:I.391, C:V.393 Hydrogen bonds: A:A.388, A:S.413, A:A.431, A:R.448, A:R.448, A:R.448, A:R.450, C:Y.395, B:Y.457, B:Y.457 Water bridges: A:R.448, A:R.448, C:N.394 pi-Cation interactions: A:R.450 Salt bridges: B:K.454

3 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.6: 28 residues within 4Å: Chain A: L.17, A.18, A.19, G.20, R.24, K.31, Q.81, Q.84, L.85, G.86, T.87, A.90, A.109, G.110, D.111, T.112, Y.147, G.148, E.163, N.178, T.179, Y.206, I.207, T.208, G.234, N.236 Ligands: CA.1, CA.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:E.163, A:Y.206 Hydrogen bonds: A:A.19, A:G.20, A:R.24, A:Q.81, A:Q.81, A:G.86, A:G.110, A:D.111, A:G.148, A:G.148, A:E.163, A:E.163, A:N.178, A:T.179, A:N.236 Water bridges: A:K.31, A:K.31, A:D.111, A:Q.202, A:N.236, A:N.236 Salt bridges: A:K.31 UD1.12: 28 residues within 4Å: Chain B: L.17, A.18, A.19, G.20, R.24, K.31, Q.81, Q.84, L.85, G.86, T.87, A.90, A.109, G.110, D.111, T.112, Y.147, G.148, E.163, N.178, T.179, Y.206, I.207, T.208, G.234, N.236 Ligands: CA.7, CA.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:E.163, B:Y.206 Hydrogen bonds: B:A.19, B:G.20, B:R.24, B:Q.81, B:Q.81, B:G.86, B:G.110, B:D.111, B:G.148, B:G.148, B:E.163, B:E.163, B:N.178, B:T.179, B:N.236 Water bridges: B:K.31, B:K.31, B:D.111, B:Q.202, B:N.236, B:N.236 Salt bridges: B:K.31 UD1.18: 28 residues within 4Å: Chain C: L.17, A.18, A.19, G.20, R.24, K.31, Q.81, Q.84, L.85, G.86, T.87, A.90, A.109, G.110, D.111, T.112, Y.147, G.148, E.163, N.178, T.179, Y.206, I.207, T.208, G.234, N.236 Ligands: CA.13, CA.14 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:E.163, C:Y.206 Hydrogen bonds: C:A.19, C:G.20, C:R.24, C:Q.81, C:Q.81, C:G.86, C:G.110, C:D.111, C:G.148, C:G.148, C:E.163, C:E.163, C:N.178, C:T.179, C:N.236 Water bridges: C:K.31, C:K.31, C:D.111, C:D.111, C:Q.202, C:N.236 Salt bridges: C:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sulzenbacher, G. et al., Crystal structure of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase bound to acetyl-coenzyme A reveals a novel active site architecture. J.Biol.Chem. (2001)

Release Date

2001-11-30

Peptides

UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE

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