SMTL ID : 6u7a.1 (3 other biounits)

Rv3722c in complex with kynurenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

1 x Q0P: (2S)-4-(2-aminophenyl)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxobutanoic acid(Non-covalent)

Q0P.1: 20 residues within 4Å: Chain A: R.36, G.37, K.38, S.99, S.100, L.101, Y.139, R.141, V.184, N.189, D.218, A.220, Y.221, S.254, S.256, K.257, F.349, R.392 Chain B: Y.69, I.287 33 PLIP interactions: 27 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:R.36, A:R.36, A:Y.139, A:V.184, A:A.220, A:Y.221, B:Y.69, B:Y.69, B:Y.69, B:I.287 Hydrogen bonds: A:R.36, A:G.37, A:G.37, A:G.37, A:S.100, A:L.101, A:R.141, A:N.189, A:Y.221, A:Y.221, A:S.254, A:S.256, A:K.257, B:Y.69 Water bridges: A:S.99, A:S.100, A:S.100, A:S.100, B:Y.69 Salt bridges: A:R.36, A:K.257, A:R.392 pi-Stacking: A:Y.139

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.59, D.65 Chain B: A.41, F.397 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.65, A:D.65 Water bridges: A:D.65, A:D.65 Salt bridges: A:R.59

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: D.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.305 GOL.4: 4 residues within 4Å: Chain A: E.169, R.201, R.202, Q.205 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.169, A:R.201, A:R.201, A:R.202, A:Q.205 GOL.8: 4 residues within 4Å: Chain B: G.71, Q.72, H.73, G.74 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.72, B:H.73, B:H.73 Water bridges: B:T.64, B:R.79, B:R.79 GOL.9: 7 residues within 4Å: Chain B: G.87, I.88, A.89, N.92, D.235, L.237, G.238 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.89, B:D.235 Water bridges: B:L.237

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 4 residues within 4Å: Chain A: Q.49, F.300, F.301, G.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.49 Water bridges: A:H.310, A:R.313 1PE.10: 6 residues within 4Å: Chain B: E.42, D.45, L.46, R.313, Q.316, I.317 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.42

1 x KYA: 4-hydroxyquinoline-2-carboxylic acid(Non-covalent)

KYA.6: 10 residues within 4Å: Chain A: Y.69, I.287 Chain B: G.37, K.38, Y.139, R.141, Y.221, K.257, F.349 Ligands: PMP.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.139, B:F.349, A:Y.69 Hydrogen bonds: B:Y.139

1 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.7: 16 residues within 4Å: Chain A: Y.69 Chain B: S.99, S.100, L.101, M.104, Y.139, H.142, V.184, N.189, D.218, A.220, Y.221, S.254, S.256, K.257 Ligands: KYA.6 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.139, B:V.184, B:A.220, B:Y.221 Hydrogen bonds: B:S.100, B:S.100, B:L.101, B:N.189, B:Y.221, B:S.254, B:S.256, B:K.257, A:Y.69 Water bridges: B:S.100, B:S.100, B:S.100, B:G.262 pi-Stacking: B:Y.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jansen, R.S. et al., Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat Commun (2020)

Release Date

2020-05-06

Peptides

Aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminotransferase

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