SMTL ID : 4ymz.1

DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.1: 14 residues within 4Å: Chain A: N.10, K.12, H.97, E.169, A.173, I.174, G.175, G.216, S.217, L.236, V.237, G.238, G.239 Ligands: SO4.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.10, A:K.12, A:H.97, A:G.175, A:S.217, A:G.238, A:G.239 Water bridges: A:V.218, A:A.240 Salt bridges: A:K.12 13P.12: 14 residues within 4Å: Chain B: N.10, K.12, H.97, E.169, A.173, I.174, G.175, G.216, S.217, L.236, V.237, G.238, G.239 Ligands: SO4.13 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.10, B:K.12, B:G.175, B:S.217, B:G.238, B:G.239 Water bridges: B:V.218, B:V.218, B:A.240 Salt bridges: B:K.12

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 10 residues within 4Å: Chain A: K.12, A.173, I.174, G.175, G.216, S.217, V.237, G.238, G.239 Ligands: 13P.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.175, A:S.217, A:G.238, A:G.239 Water bridges: A:K.12, A:V.218, A:A.240 Salt bridges: A:K.12 SO4.13: 10 residues within 4Å: Chain B: K.12, A.173, I.174, G.175, G.216, S.217, V.237, G.238, G.239 Ligands: 13P.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.175, B:S.217, B:G.238, B:G.239 Water bridges: B:V.218, B:V.218 Salt bridges: B:K.12

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

EDO.3: 4 residues within 4Å: Chain A: E.50, N.51 Chain B: E.50, N.51 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: R.116, K.120, I.156, F.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.116 EDO.5: 3 residues within 4Å: Chain A: S.204, E.208 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.205, A:E.208 EDO.6: 4 residues within 4Å: Chain A: S.146, S.147, R.150, E.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.146 Water bridges: A:S.147 EDO.7: 7 residues within 4Å: Chain A: K.4, S.162, L.164, I.165, S.209, I.210, S.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.209, A:S.211 EDO.8: 6 residues within 4Å: Chain A: P.220, D.221, N.222, I.223, Q.224, D.225 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.220, A:Q.224, A:Q.224, A:D.225, A:D.225 Water bridges: A:D.225 EDO.9: 6 residues within 4Å: Chain A: F.103, L.104, G.105 Chain B: L.104, G.105, F.110 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: L.142, E.143, F.191 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain B: R.116, K.120, G.155, I.156, F.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.116 EDO.15: 2 residues within 4Å: Chain B: G.202 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.202 EDO.16: 1 residues within 4Å: Ligands: EDO.15 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: V.159, F.160, N.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.162, B:N.163 EDO.18: 3 residues within 4Å: Chain B: H.70, F.117, K.120 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain A: G.105, F.110 Chain B: F.103, L.104 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pareek, V. et al., Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme. Chembiochem (2016)

Release Date

2016-03-09

Peptides

Triosephosphate isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Triosephosphate isomerase