SMTL ID : 5ab8.1

High resolution X-ray structure of the N-terminal truncated form (residues 1-11) of Mycobacterium tuberculosis HbN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 23 residues within 4Å: Chain A: F.34, F.35, T.38, R.42, L.43, K.46, Q.47, F.50, Y.61, G.63, A.64, M.66, V.69, H.70, R.73, I.75, H.79, F.80, V.83, I.108, A.112 Ligands: FMT.2, GOL.4 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:F.34, A:F.35, A:F.35, A:L.43, A:K.46, A:F.50, A:F.50, A:V.69, A:V.69, A:I.75, A:I.75, A:F.80, A:V.83, A:A.112 Hydrogen bonds: A:Y.61, A:A.64 Water bridges: A:G.37, A:R.42, A:R.42, A:R.42, A:R.42, A:R.42, A:R.73 Salt bridges: A:R.42, A:R.73 Metal complexes: A:H.70 HEM.6: 23 residues within 4Å: Chain B: F.34, F.35, T.38, R.42, L.43, K.46, Q.47, F.50, Y.61, G.63, A.64, M.66, V.69, H.70, R.73, I.75, H.79, F.80, V.83, I.108, A.112 Ligands: FMT.7, GOL.9 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:F.34, B:F.35, B:F.35, B:L.43, B:K.46, B:F.50, B:F.50, B:V.69, B:V.69, B:I.75, B:I.75, B:F.80, B:V.83, B:A.112 Hydrogen bonds: B:A.64 Water bridges: B:G.37, B:R.42, B:R.42, B:R.42, B:R.42, B:R.42, B:R.73 Salt bridges: B:R.42, B:R.73 Metal complexes: B:H.70

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

FMT.2: 6 residues within 4Å: Chain A: F.21, Y.22, F.35, Q.47, H.70 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.22, A:Q.47 FMT.7: 6 residues within 4Å: Chain B: F.21, Y.22, F.35, Q.47, H.70 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.47

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 1 residues within 4Å: Chain A: F.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.50 ACT.8: 1 residues within 4Å: Chain B: F.50 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.50

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.37, T.38, N.39, R.42 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.39, A:R.42 Water bridges: A:G.37, A:G.37, A:T.38, A:N.39, A:N.39, A:R.42, A:R.73 GOL.5: 6 residues within 4Å: Chain A: K.67, H.70, Q.71 Chain B: M.77, H.78, S.81 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.70, B:H.78, B:H.78, B:S.81 Water bridges: A:K.67, A:K.67, A:G.72, A:I.75, A:V.113, A:D.114 GOL.9: 5 residues within 4Å: Chain B: G.37, T.38, N.39, R.42 Ligands: HEM.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.39, B:R.42, B:R.42 Water bridges: B:G.37, B:G.37, B:T.38, B:N.39, B:N.39, B:R.73 GOL.10: 6 residues within 4Å: Chain A: M.77, H.78, S.81 Chain B: K.67, H.70, Q.71 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.70, A:H.78, A:S.81 Water bridges: B:K.67, B:K.67, B:G.72, B:I.75, B:V.113, B:D.114, A:H.78, A:H.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pesce, A. et al., The N-Terminal Pre-A Region of Mycobacterium Tuberculosis 2/2Hbn Promotes No-Dioxygenase Activity. FEBS J. (2016)

Release Date

2015-11-04

Peptides

GROUP 1 TRUNCATED HEMOGLOBIN GLBN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GROUP 1 TRUNCATED HEMOGLOBIN GLBN