SMTL ID : 3hys.1

Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 6 residues within 4Å: Chain A: T.58, R.177, W.203, L.271, F.274 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.203 Water bridges: A:R.177 Salt bridges: A:R.177 MLA.7: 7 residues within 4Å: Chain B: G.51, R.52, S.118, M.119, R.151, F.154, H.270 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.52 Hydrogen bonds: B:R.52, B:S.118, B:S.118, B:M.119 Water bridges: B:R.151, B:R.151 Salt bridges: B:R.151, B:H.270

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: G.51, R.52, S.118, M.119, R.144, Q.214, L.215 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.52, A:M.119, A:Q.214 Water bridges: A:R.52, A:R.144, A:R.144, A:R.144, A:H.270

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

EDO.3: 6 residues within 4Å: Chain A: R.52, G.54, T.58, I.205, L.271 Ligands: MLA.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.51, A:G.51 EDO.4: 3 residues within 4Å: Chain A: A.192, D.195, W.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 EDO.5: 8 residues within 4Å: Chain A: L.35, F.77, N.79, R.80, M.96, D.99, T.100, I.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.80 EDO.8: 5 residues within 4Å: Chain B: T.58, R.177, W.203, L.271, F.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.177 EDO.9: 6 residues within 4Å: Chain B: G.53, G.54, A.55, R.57, W.203, P.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.55, B:P.204 EDO.10: 5 residues within 4Å: Chain A: L.179, L.187, V.193 Chain B: R.149, A.150 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.175, A:R.175, A:L.187, A:D.190 EDO.11: 5 residues within 4Å: Chain B: G.43, D.44, A.70, G.71, Y.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.44, B:D.44 Water bridges: B:R.113

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: A.254, D.255, L.257, G.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.254, A:G.260 NA.12: 5 residues within 4Å: Chain B: A.254, D.255, L.257, P.258, G.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.258, B:G.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnston, J.M. et al., Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-06-02

Peptides

protein Rv0554, putative Bromoperoxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

protein Rv0554, putative Bromoperoxidase

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