SMTL ID : 3c4v.3 (2 other biounits)

Structure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.304, A:A.306, A:T.330, H2O.1, H2O.2 MG.3: 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:R.304, B:A.306, B:T.330, H2O.2, H2O.3 MG.6: 4 residues within 4Å: Chain C: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:R.304, C:A.306, C:T.330, H2O.3, H2O.4 MG.8: 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:R.304, D:A.306, D:T.330, H2O.5, H2O.6 MG.11: 4 residues within 4Å: Chain E: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:R.304, E:A.306, E:T.330, H2O.6, H2O.7 MG.13: 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:R.304, F:A.306, F:T.330, H2O.8, H2O.8 MG.16: 4 residues within 4Å: Chain G: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:R.304, G:A.306, G:T.330, H2O.9, H2O.10 MG.18: 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:R.304, H:A.306, H:T.330, H2O.10, H2O.11 MG.21: 4 residues within 4Å: Chain I: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:R.304, I:A.306, I:T.330, H2O.11, H2O.12 MG.23: 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:R.304, J:A.306, J:T.330, H2O.13, H2O.14 MG.26: 4 residues within 4Å: Chain K: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:R.304, K:A.306, K:T.330, H2O.14, H2O.15 MG.28: 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:R.304, L:A.306, L:T.330, H2O.16, H2O.16 MG.31: 4 residues within 4Å: Chain M: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:R.304, M:A.306, M:T.330, H2O.17, H2O.18 MG.33: 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:R.304, N:A.306, N:T.330, H2O.18, H2O.19 MG.36: 4 residues within 4Å: Chain O: Y.303, R.304, A.306, T.330 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:R.304, O:A.306, O:T.330, H2O.20, H2O.21 MG.38: 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:R.304, P:A.306, P:T.330, H2O.21, H2O.22

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

UDP.2: 18 residues within 4Å: Chain A: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, A:Y.202, A:R.294, A:R.294, A:E.316, A:S.317, A:L.320, A:V.321, A:E.324 Salt bridges: A:R.231, A:K.236, A:K.236 UDP.4: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.5 15 PLIP interactions: 15 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:E.316, B:S.317, B:L.320, B:V.321, B:E.324 Salt bridges: B:R.231, B:K.236, B:K.236 UDP.7: 18 residues within 4Å: Chain C: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, C:Y.202, C:R.294, C:R.294, C:E.316, C:S.317, C:L.320, C:V.321, C:E.324 Salt bridges: C:R.231, C:K.236, C:K.236 UDP.9: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.10 15 PLIP interactions: 15 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:E.316, D:S.317, D:L.320, D:V.321, D:E.324 Salt bridges: D:R.231, D:K.236, D:K.236 UDP.12: 18 residues within 4Å: Chain E: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, E:Y.202, E:R.294, E:R.294, E:E.316, E:S.317, E:L.320, E:V.321, E:E.324 Salt bridges: E:R.231, E:K.236, E:K.236 UDP.14: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.15 15 PLIP interactions: 15 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:E.316, F:S.317, F:L.320, F:V.321, F:E.324 Salt bridges: F:R.231, F:K.236, F:K.236 UDP.17: 18 residues within 4Å: Chain G: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, G:Y.202, G:R.294, G:R.294, G:E.316, G:S.317, G:L.320, G:V.321, G:E.324 Salt bridges: G:R.231, G:K.236, G:K.236 UDP.19: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.20 15 PLIP interactions: 15 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:E.316, H:S.317, H:L.320, H:V.321, H:E.324 Salt bridges: H:R.231, H:K.236, H:K.236 UDP.22: 18 residues within 4Å: Chain I: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, I:Y.202, I:Y.202, I:R.294, I:R.294, I:E.316, I:S.317, I:L.320, I:V.321, I:E.324 Salt bridges: I:R.231, I:K.236, I:K.236 UDP.24: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.25 14 PLIP interactions: 14 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:E.316, J:S.317, J:L.320, J:V.321, J:E.324 Salt bridges: J:R.231, J:K.236, J:K.236 UDP.27: 18 residues within 4Å: Chain K: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, K:Y.202, K:Y.202, K:R.294, K:R.294, K:E.316, K:S.317, K:L.320, K:V.321, K:E.324 Salt bridges: K:R.231, K:K.236, K:K.236 UDP.29: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.30 14 PLIP interactions: 14 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:E.316, L:S.317, L:L.320, L:V.321, L:E.324 Salt bridges: L:R.231, L:K.236, L:K.236 UDP.32: 18 residues within 4Å: Chain M: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, M:Y.202, M:Y.202, M:R.294, M:R.294, M:E.316, M:S.317, M:L.320, M:V.321, M:E.324 Salt bridges: M:R.231, M:K.236, M:K.236 UDP.34: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.35 14 PLIP interactions: 14 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:E.316, N:S.317, N:L.320, N:V.321, N:E.324 Salt bridges: N:R.231, N:K.236, N:K.236 UDP.37: 18 residues within 4Å: Chain O: Q.15, P.16, G.22, G.23, V.26, Y.202, V.229, R.231, K.236, C.262, P.293, R.294, L.299, E.316, S.317, 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.23, O:Y.202, O:Y.202, O:R.294, O:R.294, O:E.316, O:S.317, O:L.320, O:V.321, O:E.324 Salt bridges: O:R.231, O:K.236, O:K.236 UDP.39: 21 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, S.317, G.319, L.320, V.321, E.324 Ligands: LIP.40 14 PLIP interactions: 14 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:E.316, P:S.317, P:L.320, P:V.321, P:E.324 Salt bridges: P:R.231, P:K.236, P:K.236

8 x LIP: L-MYO-INOSITOL-1-PHOSPHATE(Non-covalent)

LIP.5: 15 residues within 4Å: Chain B: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.20, B:G.22, B:G.23, B:M.24, B:K.78, B:K.78, B:Y.110, B:Y.110, B:T.134, B:R.231 Salt bridges: B:K.78, B:R.154 LIP.10: 15 residues within 4Å: Chain D: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.9 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.20, D:G.22, D:G.23, D:M.24, D:K.78, D:K.78, D:Y.110, D:Y.110, D:T.134, D:R.231 Salt bridges: D:K.78, D:R.154 LIP.15: 15 residues within 4Å: Chain F: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.14 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:D.20, F:G.22, F:G.23, F:M.24, F:K.78, F:K.78, F:Y.110, F:Y.110, F:T.134, F:R.231 Salt bridges: F:K.78, F:R.154 LIP.20: 15 residues within 4Å: Chain H: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.19 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:D.20, H:G.22, H:G.23, H:M.24, H:K.78, H:K.78, H:Y.110, H:Y.110, H:T.134, H:R.231 Salt bridges: H:K.78, H:R.154 LIP.25: 15 residues within 4Å: Chain J: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.24 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:D.20, J:G.22, J:G.23, J:M.24, J:K.78, J:K.78, J:Y.110, J:T.134, J:T.134, J:R.231 Salt bridges: J:K.78, J:R.154 LIP.30: 15 residues within 4Å: Chain L: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.29 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:D.20, L:G.22, L:G.23, L:M.24, L:K.78, L:K.78, L:Y.110, L:T.134, L:T.134, L:R.231 Salt bridges: L:K.78, L:R.154 LIP.35: 15 residues within 4Å: Chain N: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.34 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:D.20, N:G.22, N:G.23, N:M.24, N:K.78, N:K.78, N:Y.110, N:T.134, N:T.134, N:R.231 Salt bridges: N:K.78, N:R.154 LIP.40: 15 residues within 4Å: Chain P: H.9, T.10, D.20, G.22, G.23, M.24, N.25, K.78, Y.110, H.133, T.134, R.154, R.231, F.235 Ligands: UDP.39 12 PLIP interactions: 12 interactions with chain P Hydrogen bonds: P:D.20, P:G.22, P:G.23, P:M.24, P:K.78, P:K.78, P:Y.110, P:T.134, P:T.134, P:R.231 Salt bridges: P:K.78, P:R.154

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