SMTL ID : 4k6r.1

Crystal structure of GlmU in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: A.20, G.21, P.22, G.23, T.24, R.25, G.63, H.64, Q.89, R.91, P.92, L.93, G.94, T.95, A.98, E.213 Ligands: MG.2, MG.3, GN1.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.23, A:T.24, A:R.25, A:H.64, A:Q.89, A:G.94 Water bridges: A:A.20, A:G.21, A:G.21, A:R.25, A:R.25, A:R.25, A:R.25, A:K.32, A:K.32, A:K.32, A:H.64, A:E.213, A:N.245 Salt bridges: A:R.25, A:R.25, A:K.32 ATP.9: 19 residues within 4Å: Chain B: A.20, G.21, P.22, G.23, T.24, R.25, G.63, H.64, Q.89, R.91, P.92, L.93, G.94, T.95, A.98, E.213 Ligands: MG.10, MG.11, GN1.12 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.23, B:T.24, B:R.25, B:H.64, B:Q.89, B:G.94 Water bridges: B:A.20, B:G.21, B:G.21, B:R.25, B:R.25, B:R.25, B:R.25, B:K.32, B:K.32, B:K.32, B:H.64, B:E.213, B:N.245 Salt bridges: B:R.25, B:R.25, B:K.32 ATP.17: 19 residues within 4Å: Chain C: A.20, G.21, P.22, G.23, T.24, R.25, G.63, H.64, Q.89, R.91, P.92, L.93, G.94, T.95, A.98, E.213 Ligands: MG.18, MG.19, GN1.20 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.23, C:T.24, C:R.25, C:H.64, C:Q.89, C:G.94 Water bridges: C:A.20, C:G.21, C:G.21, C:R.25, C:R.25, C:R.25, C:R.25, C:K.32, C:K.32, C:K.32, C:H.64, C:E.213, C:N.245 Salt bridges: C:R.25, C:R.25, C:K.32

12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: GN1.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.120, H2O.13, H2O.13, H2O.13 MG.7: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.6, CO.14, MG.15, CO.22, MG.23 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.423, B:D.423, C:D.423, H2O.1, H2O.19, H2O.37 MG.10: 1 residues within 4Å: Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: GN1.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.120, H2O.31, H2O.31, H2O.31 MG.15: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.6, MG.7, CO.14, CO.22, MG.23 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.423, B:D.423, C:D.423, H2O.1, H2O.19, H2O.37 MG.18: 1 residues within 4Å: Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: GN1.20 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.120, H2O.49, H2O.49, H2O.49 MG.23: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.6, MG.7, CO.14, MG.15, CO.22 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.1, H2O.19, H2O.37

6 x GN1: 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GN1.4: 13 residues within 4Å: Chain A: R.25, T.95, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: ATP.1, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.172, A:Y.215 Hydrogen bonds: A:R.25, A:G.157, A:E.172, A:E.172, A:N.187, A:N.245 Water bridges: A:R.25, A:S.118, A:S.118, A:S.118, A:T.121, A:E.172, A:E.172, A:A.188, A:V.244 GN1.8: 11 residues within 4Å: Chain A: R.350, K.368, Y.383, V.400, N.403, Y.404, K.409 Chain B: P.379, H.380, N.394, A.397 21 PLIP interactions: 7 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:A.397, A:Y.383, A:V.400 Hydrogen bonds: B:H.380, B:N.394, B:N.394, A:Y.383, A:N.403, A:K.409 Water bridges: B:H.380, B:I.395, A:R.350, A:R.350, A:R.350, A:K.368 Salt bridges: B:H.380, A:R.350, A:K.368, A:K.368, A:K.409, A:K.409 GN1.12: 13 residues within 4Å: Chain B: R.25, T.95, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: ATP.9, MG.13 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:E.172, B:Y.215 Hydrogen bonds: B:R.25, B:G.157, B:E.172, B:E.172, B:N.187, B:N.245 Water bridges: B:R.25, B:S.118, B:S.118, B:S.118, B:T.121, B:E.172, B:E.172, B:A.188, B:V.244 GN1.16: 11 residues within 4Å: Chain B: R.350, K.368, Y.383, V.400, N.403, Y.404, K.409 Chain C: P.379, H.380, N.394, A.397 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:Y.383, B:V.400, C:A.397 Hydrogen bonds: B:Y.383, B:N.403, B:K.409, C:H.380, C:N.394, C:N.394 Water bridges: B:R.350, B:R.350, B:R.350, B:K.368, C:H.380, C:I.395 Salt bridges: B:R.350, B:K.368, B:K.368, B:K.409, B:K.409, C:H.380 GN1.20: 13 residues within 4Å: Chain C: R.25, T.95, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: ATP.17, MG.21 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:E.172, C:Y.215 Hydrogen bonds: C:R.25, C:G.157, C:E.172, C:E.172, C:N.187, C:N.245 Water bridges: C:R.25, C:S.118, C:S.118, C:S.118, C:T.121, C:E.172, C:E.172, C:A.188, C:V.244 GN1.24: 11 residues within 4Å: Chain A: P.379, H.380, N.394, A.397 Chain C: R.350, K.368, Y.383, V.400, N.403, Y.404, K.409 21 PLIP interactions: 7 interactions with chain A, 14 interactions with chain C Hydrophobic interactions: A:A.397, C:Y.383, C:V.400 Hydrogen bonds: A:H.380, A:N.394, A:N.394, C:Y.383, C:N.403, C:K.409 Water bridges: A:H.380, A:I.395, C:R.350, C:R.350, C:R.350, C:K.368 Salt bridges: A:H.380, C:R.350, C:K.368, C:K.368, C:K.409, C:K.409

3 x CO: COBALT (II) ION(Non-covalent)

CO.6: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.7, CO.14, MG.15, CO.22, MG.23 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.423, A:D.423, C:D.423, H2O.14, H2O.33 CO.14: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.6, MG.7, MG.15, CO.22, MG.23 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.423, A:D.423, C:D.423, H2O.33, H2O.51 CO.22: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.6, MG.7, CO.14, MG.15, MG.23 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.14, H2O.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vithani, N. et al., GlmU (N-acetylglucosamine-1-phosphate uridyltransferase) bound to three magnesium ions and ATP at the active site. Acta Crystallogr.,Sect.F (2014)

Release Date

2014-04-16

Peptides

Bifunctional protein GlmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein GlmU

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