SMTL ID : 3c4q.3 (2 other biounits)

Structure of the retaining glycosyltransferase MshA : The first step in mycothiol biosynthesis. Organism : Corynebacterium glutamicum- Complex with UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-16-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.303, A:R.304, A:A.306, A:T.330, H2O.1 MG.4: 4 residues within 4Å: Chain B: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.303, B:A.306, B:T.330, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain C: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.303, C:R.304, C:A.306, C:T.330, H2O.3 MG.10: 4 residues within 4Å: Chain D: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Y.303, D:A.306, D:T.330, H2O.4, H2O.4 MG.13: 4 residues within 4Å: Chain E: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:Y.303, E:R.304, E:A.306, E:T.330, H2O.5 MG.16: 4 residues within 4Å: Chain F: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:Y.303, F:A.306, F:T.330, H2O.6, H2O.7 MG.19: 4 residues within 4Å: Chain G: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:Y.303, G:R.304, G:A.306, G:T.330, H2O.7 MG.22: 4 residues within 4Å: Chain H: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:Y.303, H:A.306, H:T.330, H2O.8, H2O.9 MG.25: 4 residues within 4Å: Chain I: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:Y.303, I:R.304, I:A.306, I:T.330, H2O.9 MG.28: 4 residues within 4Å: Chain J: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:Y.303, J:A.306, J:T.330, H2O.10, H2O.11 MG.31: 4 residues within 4Å: Chain K: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:Y.303, K:R.304, K:A.306, K:T.330, H2O.11 MG.34: 4 residues within 4Å: Chain L: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:Y.303, L:A.306, L:T.330, H2O.12, H2O.13 MG.37: 4 residues within 4Å: Chain M: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:Y.303, M:R.304, M:A.306, M:T.330, H2O.13 MG.40: 4 residues within 4Å: Chain N: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:Y.303, N:A.306, N:T.330, H2O.14, H2O.15 MG.43: 4 residues within 4Å: Chain O: Y.303, R.304, A.306, T.330 5 PLIP interactions: 4 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:Y.303, O:R.304, O:A.306, O:T.330, H2O.15 MG.46: 4 residues within 4Å: Chain P: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:Y.303, P:A.306, P:T.330, H2O.16, H2O.17

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

SO4.2: 5 residues within 4Å: Chain A: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain B: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain C: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain D: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain E: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain F: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain G: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain H: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain I: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain J: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain K: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain L: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain M: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain N: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain O: K.78, Y.110, T.134, R.154, F.235 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain P: K.78, Y.110, T.134, R.154 Ligand excluded by PLIP

16 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 19 residues within 4Å: Chain A: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.229 Hydrogen bonds: A:Q.15, A:G.17, A:G.23, A:Y.202, A:R.294, A:R.294, A:L.320, A:V.321, A:E.324 Water bridges: A:S.317 Salt bridges: A:R.231, A:K.236, A:K.236 UDP.6: 19 residues within 4Å: Chain B: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.229 Hydrogen bonds: B:Q.15, B:G.23, B:Y.202, B:Y.202, B:R.294, B:R.294, B:L.320, B:V.321, B:E.324 Water bridges: B:S.317 Salt bridges: B:R.231, B:K.236, B:K.236 UDP.9: 19 residues within 4Å: Chain C: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.229 Hydrogen bonds: C:Q.15, C:G.17, C:G.23, C:Y.202, C:R.294, C:R.294, C:L.320, C:V.321, C:E.324 Water bridges: C:S.317 Salt bridges: C:R.231, C:K.236, C:K.236 UDP.12: 19 residues within 4Å: Chain D: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.229 Hydrogen bonds: D:Q.15, D:G.23, D:Y.202, D:Y.202, D:R.294, D:R.294, D:L.320, D:V.321, D:E.324 Water bridges: D:S.317 Salt bridges: D:R.231, D:K.236, D:K.236 UDP.15: 19 residues within 4Å: Chain E: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:V.229 Hydrogen bonds: E:Q.15, E:G.17, E:G.23, E:Y.202, E:R.294, E:R.294, E:L.320, E:V.321, E:E.324 Water bridges: E:S.317 Salt bridges: E:R.231, E:K.236, E:K.236 UDP.18: 19 residues within 4Å: Chain F: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:V.229 Hydrogen bonds: F:Q.15, F:G.23, F:Y.202, F:Y.202, F:R.294, F:R.294, F:L.320, F:V.321, F:E.324 Water bridges: F:S.317 Salt bridges: F:R.231, F:K.236, F:K.236 UDP.21: 19 residues within 4Å: Chain G: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:V.229 Hydrogen bonds: G:Q.15, G:G.17, G:G.23, G:Y.202, G:R.294, G:R.294, G:L.320, G:V.321, G:E.324 Water bridges: G:S.317 Salt bridges: G:R.231, G:K.236, G:K.236 UDP.24: 19 residues within 4Å: Chain H: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:V.229 Hydrogen bonds: H:Q.15, H:G.23, H:Y.202, H:Y.202, H:R.294, H:R.294, H:L.320, H:V.321, H:E.324 Water bridges: H:S.317 Salt bridges: H:R.231, H:K.236, H:K.236 UDP.27: 19 residues within 4Å: Chain I: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 15 PLIP interactions: 15 interactions with chain I Hydrophobic interactions: I:V.229 Hydrogen bonds: I:Q.15, I:G.17, I:G.23, I:Y.202, I:Y.202, I:R.294, I:R.294, I:L.320, I:V.321, I:E.324 Water bridges: I:S.317 Salt bridges: I:R.231, I:K.236, I:K.236 UDP.30: 19 residues within 4Å: Chain J: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:V.229 Hydrogen bonds: J:Q.15, J:G.23, J:Y.202, J:R.294, J:R.294, J:L.320, J:V.321, J:E.324 Water bridges: J:S.317 Salt bridges: J:R.231, J:K.236, J:K.236 UDP.33: 19 residues within 4Å: Chain K: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 15 PLIP interactions: 15 interactions with chain K Hydrophobic interactions: K:V.229 Hydrogen bonds: K:Q.15, K:G.17, K:G.23, K:Y.202, K:Y.202, K:R.294, K:R.294, K:L.320, K:V.321, K:E.324 Water bridges: K:S.317 Salt bridges: K:R.231, K:K.236, K:K.236 UDP.36: 19 residues within 4Å: Chain L: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:V.229 Hydrogen bonds: L:Q.15, L:G.23, L:Y.202, L:R.294, L:R.294, L:L.320, L:V.321, L:E.324 Water bridges: L:S.317 Salt bridges: L:R.231, L:K.236, L:K.236 UDP.39: 19 residues within 4Å: Chain M: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 15 PLIP interactions: 15 interactions with chain M Hydrophobic interactions: M:V.229 Hydrogen bonds: M:Q.15, M:G.17, M:G.23, M:Y.202, M:Y.202, M:R.294, M:R.294, M:L.320, M:V.321, M:E.324 Water bridges: M:S.317 Salt bridges: M:R.231, M:K.236, M:K.236 UDP.42: 19 residues within 4Å: Chain N: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 13 PLIP interactions: 13 interactions with chain N Hydrophobic interactions: N:V.229 Hydrogen bonds: N:Q.15, N:G.23, N:Y.202, N:R.294, N:R.294, N:L.320, N:V.321, N:E.324 Water bridges: N:S.317 Salt bridges: N:R.231, N:K.236, N:K.236 UDP.45: 19 residues within 4Å: Chain O: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, G.230, R.231, K.236, C.262, P.293, R.294, L.299, E.316, L.320, V.321, E.324 15 PLIP interactions: 15 interactions with chain O Hydrophobic interactions: O:V.229 Hydrogen bonds: O:Q.15, O:G.17, O:G.23, O:Y.202, O:Y.202, O:R.294, O:R.294, O:L.320, O:V.321, O:E.324 Water bridges: O:S.317 Salt bridges: O:R.231, O:K.236, O:K.236 UDP.48: 19 residues within 4Å: Chain P: Q.15, P.16, G.17, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, G.319, L.320, V.321, E.324 13 PLIP interactions: 13 interactions with chain P Hydrophobic interactions: P:V.229 Hydrogen bonds: P:Q.15, P:G.23, P:Y.202, P:R.294, P:R.294, P:L.320, P:V.321, P:E.324 Water bridges: P:S.317 Salt bridges: P:R.231, P:K.236, P:K.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Structural and Enzymatic Analysis of MshA from Corynebacterium glutamicum: SUBSTRATE-ASSISTED CATALYSIS. J.Biol.Chem. (2008)

Release Date

2008-04-01

Peptides

Predicted glycosyltransferases: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

M
A

N
B

O
A

P
B

Predicted glycosyltransferases

Related Entries With Identical Sequence