SMTL ID : 8b5k.2 (1 other biounit)

Structure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 6.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: I.14, S.32, Y.33 No protein-ligand interaction detected (PLIP) FMT.3: 5 residues within 4Å: Chain A: T.131, D.132, Y.133, G.231, A.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.131 FMT.4: 1 residues within 4Å: Chain A: D.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.242, A:D.242 Water bridges: A:D.242 FMT.9: 3 residues within 4Å: Chain B: D.71, R.74, Y.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.71, B:D.71, B:R.74 Water bridges: B:S.66, B:Y.75 FMT.10: 4 residues within 4Å: Chain B: D.95, W.96, R.125, I.196 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.125

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: L.7, D.8, S.66, D.71, R.74, Y.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.64, A:R.74, A:R.74 GOL.5: 5 residues within 4Å: Chain A: P.222, K.223, N.249, R.251, F.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.223, A:K.223, A:R.251, A:R.251 GOL.6: 4 residues within 4Å: Chain A: R.141, R.194, E.201, P.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.141, A:R.194, A:E.201 GOL.8: 5 residues within 4Å: Chain A: D.95, W.96, R.125, I.196, I.233 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.96, A:R.125 Water bridges: A:N.28, A:H.259

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

TRS.7: 3 residues within 4Å: Chain A: P.40, H.41, R.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.41, A:H.41 Water bridges: A:R.274

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.11: 4 residues within 4Å: Chain B: P.40, H.41, D.44, R.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.44, B:R.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Snajdarova, K. et al., Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-08-30

Peptides

Haloalkane dehalogenase DhaA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Haloalkane dehalogenase DhaA

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