SMTL ID : 6y9e.1 (5 other biounits)

Crystal structure of putative ancestral haloalkane dehalogenase AncHLD2 (node 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: N.38, W.104, F.167, F.204, P.205 Ligand excluded by PLIP CL.2: 7 residues within 4Å: Chain A: H.36, G.37, T.40, I.44, Q.102, Y.272, Q.274 Ligand excluded by PLIP

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 8 residues within 4Å: Chain A: R.130, D.136, D.137, H.139, Q.140, A.244, L.245, S.247 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.140 Hydrogen bonds: A:R.130, A:D.137 Water bridges: A:H.139

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

TRS.4: 1 residues within 4Å: Chain A: E.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.183 Water bridges: A:E.183, A:E.183 TRS.5: 5 residues within 4Å: Chain A: D.86, I.89, D.90, R.115, R.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.86, A:D.90, A:R.115, A:R.116 TRS.6: 5 residues within 4Å: Chain A: P.117, D.118, V.120, T.232, Y.233 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.117, A:D.118, A:V.120, A:T.232, A:T.232, A:T.232 TRS.7: 2 residues within 4Å: Chain A: P.195, E.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.196, A:E.196, A:E.196

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

EDO.8: 3 residues within 4Å: Chain A: D.16, P.72, D.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.16, A:D.73 EDO.9: 6 residues within 4Å: Chain A: K.71, P.72, D.73, Y.76, E.196, R.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.72, A:E.196 EDO.10: 2 residues within 4Å: Chain A: M.147, S.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.170 Water bridges: A:Q.143, A:S.175, A:S.175 EDO.11: 2 residues within 4Å: Chain A: R.170, P.173 No protein-ligand interaction detected (PLIP) EDO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain A: I.7, R.22, R.46 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: R.262, E.291, I.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.262, A:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Babkova, P. et al., Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Comput Struct Biotechnol J (2020)

Release Date

2020-11-18

Peptides

Ancestral haloalkane dehalogenase AncHLD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ancestral haloalkane dehalogenase AncHLD2

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