SMTL ID : 2gl3.1

Crystal structure of Mycobacterium tuberculosis trHbN, TyrB10Phe GlnE11Val mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: Q.79, V.80, Q.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.80

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: P.108, S.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.109 Water bridges: A:E.110 PO4.3: 7 residues within 4Å: Chain A: V.34, R.35, A.38 Chain B: R.53, G.74, A.75 Ligands: HEM.8 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:R.35, A:R.35, A:R.35, B:Q.79 Salt bridges: A:R.35 Hydrogen bonds: B:R.53, B:A.75 PO4.6: 7 residues within 4Å: Chain B: G.2, L.3, R.6, Y.16, D.17, H.22, P.69 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.3, B:Y.16, B:H.22 Water bridges: B:R.6, B:R.6, B:E.23 Salt bridges: B:R.6

2 x CYN: CYANIDE ION(Non-covalent)

CYN.4: 5 residues within 4Å: Chain A: F.33, F.46, L.54, V.58 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CYN.7: 5 residues within 4Å: Chain B: F.33, F.46, L.54, V.58 Ligands: HEM.8 No protein-ligand interaction detected (PLIP)

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

HEM.5: 25 residues within 4Å: Chain A: L.42, F.45, F.46, G.48, T.49, R.53, L.54, K.57, V.58, F.61, F.62, Y.72, G.74, A.75, M.77, V.80, H.81, R.84, I.86, H.90, F.91, V.94, I.119, V.126 Ligands: CYN.4 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:L.42, A:F.45, A:F.45, A:F.46, A:F.46, A:T.49, A:L.54, A:V.58, A:F.61, A:F.61, A:F.62, A:Y.72, A:V.80, A:V.80, A:I.86, A:I.86, A:I.86, A:H.90, A:F.91, A:V.94, A:V.94, A:I.119, A:V.126 Hydrogen bonds: A:Y.72, A:A.75 Water bridges: A:T.49, A:R.53 Salt bridges: A:R.53, A:R.84 Metal complexes: A:H.81 HEM.8: 25 residues within 4Å: Chain B: L.42, F.45, F.46, T.49, R.53, L.54, K.57, V.58, F.61, F.62, Y.72, G.74, A.75, M.77, V.80, H.81, R.84, I.86, H.90, F.91, V.94, I.119, V.126 Ligands: PO4.3, CYN.7 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:L.42, B:F.45, B:F.46, B:F.46, B:T.49, B:L.54, B:V.58, B:F.61, B:F.62, B:I.86, B:I.86, B:H.90, B:F.91, B:V.94, B:V.94, B:I.119, B:V.126 Hydrogen bonds: B:T.49, B:Y.72, B:A.75 Water bridges: B:T.49, B:R.53 Salt bridges: B:R.53, B:R.84 Metal complexes: B:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ouellet, Y. et al., Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues. Biochemistry (2006)

Release Date

2006-09-19

Peptides

Hemoglobin-like protein HbN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemoglobin-like protein HbN