SMTL ID : 6ien.1

Substrate/product bound Argininosuccinate lyase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

3 x AS1: ARGININOSUCCINATE(Non-covalent)

AS1.1: 16 residues within 4Å: Chain A: S.113, R.114, N.115, V.118, Y.322, Q.327, K.330 Chain B: T.160, H.161 Chain C: G.281, S.282, S.283, I.284, M.285, K.288, N.290 18 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 13 interactions with chain A Hydrogen bonds: C:S.283, C:N.290, B:T.160, A:S.113, A:R.114, A:R.114, A:N.115, A:N.115, A:Y.322, A:Q.327 Salt bridges: C:K.288, B:H.161, A:R.114, A:K.330 Hydrophobic interactions: A:R.114, A:V.118 Water bridges: A:S.27, A:S.27 AS1.5: 16 residues within 4Å: Chain A: T.160, H.161 Chain B: S.113, R.114, N.115, V.118, Y.322, L.326, Q.327, K.330 Chain D: G.281, S.282, S.283, M.285, K.288, N.290 17 PLIP interactions: 3 interactions with chain D, 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:S.283, D:N.290, B:S.27, B:R.114, B:R.114, B:N.115, B:N.115, B:Y.322, B:Q.327, A:T.160 Salt bridges: D:K.288, B:R.114, B:K.330, A:H.161 Hydrophobic interactions: B:R.114 Water bridges: B:D.31, B:R.324 AS1.11: 15 residues within 4Å: Chain B: S.282, S.283, M.285, K.288, N.290 Chain C: T.160, H.161 Chain D: S.113, R.114, N.115, V.118, Y.322, L.326, Q.327, K.330 18 PLIP interactions: 2 interactions with chain C, 12 interactions with chain D, 4 interactions with chain B Hydrogen bonds: C:T.160, D:D.87, D:R.114, D:N.115, D:N.115, D:Y.322, D:Y.322, D:Q.327, B:G.281, B:S.283, B:N.290 Salt bridges: C:H.161, D:R.114, D:K.330, B:K.288 Hydrophobic interactions: D:R.114, D:V.118 Water bridges: D:Q.327

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 10 residues within 4Å: Chain A: S.282, S.283, K.288, N.290 Chain C: S.113, R.114, N.115 Chain D: T.160, H.161 Ligands: ARG.9 11 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 4 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.283, A:N.290, D:T.160, C:R.114, C:N.115, C:N.115 Salt bridges: A:K.288, D:H.161, C:R.114, R.9, R.9

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

EDO.3: 4 residues within 4Å: Chain A: A.90, E.93, I.97 Chain B: R.387 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.387, A:E.93 EDO.6: 7 residues within 4Å: Chain B: D.38, S.42, L.92, E.93, L.96, L.108, R.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.38, B:S.42, B:R.112 EDO.7: 6 residues within 4Å: Chain B: T.267, E.268, R.360 Chain C: R.360, L.364 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.360, C:R.360 EDO.8: 4 residues within 4Å: Chain B: S.78, F.79, G.80, R.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.80, B:G.80, B:R.94 Water bridges: B:R.99 EDO.10: 5 residues within 4Å: Chain B: R.360, L.364 Chain C: E.268, R.360 Ligands: EDO.7 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.360, C:R.360, B:R.360, B:R.360

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: E.86, R.114 Chain C: T.280, G.281, S.282, S.283 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.280, C:S.282 Water bridges: A:R.324

1 x ARG: ARGININE(Non-covalent)

ARG.9: 10 residues within 4Å: Chain C: S.27, R.114, N.115, V.118, Y.322, L.326, Q.327, K.330 Chain D: H.161 Ligands: FUM.2 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:R.114, C:V.118 Hydrogen bonds: C:S.27, C:R.114, C:N.115, C:R.324, C:Q.327, R.9, R.9 Salt bridges: C:K.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paul, A. et al., Structural studies on M. tuberculosis argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism. IUBMB Life (2019)

Release Date

2019-02-20

Peptides

Argininosuccinate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Argininosuccinate lyase

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