SMTL ID : 4k2m.1

Crystal structure of ntda from bacillus subtilis in complex with the plp external aldimine adduct with kanosamine-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x O1G: 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco pyranose(Non-covalent)

O1G.1: 23 residues within 4Å: Chain A: S.126, G.127, T.128, S.152, F.153, A.155, T.156, V.198, D.224, C.226, Q.227, S.244, N.246, Y.248, K.249, A.257, Y.380, Y.381 Chain B: T.100, S.101, Y.276, K.284, N.294 29 PLIP interactions: 20 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.153, A:A.155, A:V.198 Hydrogen bonds: A:S.126, A:G.127, A:T.128, A:T.128, A:Q.227, A:S.244, A:N.246, A:Y.248, A:K.249, A:A.257, A:Y.381, A:Y.381, B:T.100, B:S.101, B:N.294 Water bridges: A:K.249, A:H.351, A:Y.380, B:S.101, B:S.101, B:K.284, B:K.284 Salt bridges: A:K.249, A:K.249, B:K.284, B:K.284 O1G.7: 23 residues within 4Å: Chain A: T.100, S.101, Y.276, K.284, N.294 Chain B: S.126, G.127, T.128, S.152, F.153, A.155, T.156, V.198, D.224, C.226, Q.227, S.244, N.246, Y.248, K.249, A.257, Y.380, Y.381 29 PLIP interactions: 20 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.153, B:A.155, B:V.198, B:Q.227 Hydrogen bonds: B:S.126, B:G.127, B:T.128, B:Q.227, B:S.244, B:N.246, B:Y.248, B:K.249, B:A.257, B:Y.381, B:Y.381, A:T.100, A:S.101, A:Y.276, A:N.294 Water bridges: B:K.249, B:H.351, B:Y.380, B:Y.380, A:S.101, A:S.101, A:K.284 Salt bridges: B:K.249, A:K.284, A:K.284

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

EDO.2: 7 residues within 4Å: Chain A: Q.175, F.177, E.340, L.341, P.342, P.354, K.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.175, A:P.354 Water bridges: A:E.343 EDO.3: 5 residues within 4Å: Chain A: D.378, V.379, Y.380, Y.381 Chain B: N.285 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.378, B:N.285 Water bridges: A:Y.380 EDO.5: 8 residues within 4Å: Chain A: N.151, F.177, L.200, Y.201, Y.380, L.384, H.409, V.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.151, A:Y.201, A:H.409 Water bridges: A:Y.381 EDO.6: 2 residues within 4Å: Chain A: Q.4, E.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.31, A:E.31 EDO.8: 4 residues within 4Å: Chain A: N.285 Chain B: D.378, V.379, Y.380 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.378 EDO.11: 9 residues within 4Å: Chain B: N.151, F.177, L.200, Y.201, Y.380, Y.381, L.384, H.409, V.412 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.151, B:Y.381 Water bridges: B:Y.381, B:Y.381 EDO.12: 7 residues within 4Å: Chain B: Q.175, F.177, E.340, L.341, P.342, P.354, K.356 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.175, B:P.354 Water bridges: B:E.343

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: L.72, Y.248, R.319, H.351, L.417 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.72 Hydrogen bonds: A:Y.248 Water bridges: A:L.417 Salt bridges: A:R.319, A:H.351 ACT.9: 4 residues within 4Å: Chain B: I.168, Y.169, Y.397, L.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.169 Water bridges: B:Y.169 ACT.10: 7 residues within 4Å: Chain B: L.72, Y.248, R.319, H.351, L.352, L.417, Y.418 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.72, B:L.352 Hydrogen bonds: B:H.351 Water bridges: B:L.417 Salt bridges: B:R.319, B:H.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Straaten, K.E. et al., The Structure of NtdA, a Sugar Aminotransferase Involved in the Kanosamine Biosynthetic Pathway in Bacillus subtilis, Reveals a New Subclass of Aminotransferases. J.Biol.Chem. (2013)

Release Date

2013-10-16

Peptides

NTD biosynthesis operon protein NtdA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NTD biosynthesis operon protein NtdA

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