SMTL ID : 1ngk.1

Crystallographic Structure of Mycobacterium tuberculosis Hemoglobin O

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-12-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.59, R.60, E.64 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: D.40, G.43, A.44, R.47 Chain H: P.59 Ligands: HEM.7 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: H.93 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: R.21 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.72 Chain G: R.79 Chain L: R.79 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: G.43, A.44, R.47 Chain I: P.59, R.60 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: R.72 Chain E: R.72 Chain H: R.79 Chain J: R.79 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain C: G.43, A.44, R.47 Chain G: P.59, R.60 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain C: R.21 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain D: G.43, A.44, R.47 Chain K: P.59, R.60 Ligands: HEM.18 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain E: P.59, R.60, E.64 Chain J: R.90 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain E: D.40, G.43, R.47 Chain L: G.58, P.59 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain G: S.20, R.21 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain G: R.66, R.74 Chain K: R.66, R.74 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain C: R.72 Chain F: R.72 Chain I: R.79 Chain K: R.79 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain F: G.43, A.44, R.47 Chain J: P.59, R.60 Ligands: HEM.24 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain I: R.74 Chain J: R.66, R.74 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain H: R.66 Chain L: R.66, R.74 Ligand excluded by PLIP

12 x CYN: CYANIDE ION(Non-covalent)

CYN.6: 6 residues within 4Å: Chain A: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CYN.10: 6 residues within 4Å: Chain B: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.11 No protein-ligand interaction detected (PLIP) CYN.14: 6 residues within 4Å: Chain C: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.15 No protein-ligand interaction detected (PLIP) CYN.17: 5 residues within 4Å: Chain D: Y.23, Y.36, L.48, W.88 Ligands: HEM.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.36 Water bridges: D:L.48 CYN.21: 6 residues within 4Å: Chain E: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.22 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.36, E:Y.36 Water bridges: E:L.48 CYN.23: 6 residues within 4Å: Chain F: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.24 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.36, F:W.88 CYN.27: 5 residues within 4Å: Chain G: Y.36, L.48, H.75, W.88 Ligands: HEM.28 No protein-ligand interaction detected (PLIP) CYN.29: 5 residues within 4Å: Chain H: Y.36, L.48, H.75, W.88 Ligands: HEM.30 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.36 CYN.32: 6 residues within 4Å: Chain I: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.33 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Y.36, I:W.88 CYN.36: 6 residues within 4Å: Chain J: Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.37 No protein-ligand interaction detected (PLIP) CYN.38: 6 residues within 4Å: Chain K: F.22, Y.23, Y.36, L.48, W.88 Ligands: HEM.39 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Y.23, K:Y.36 CYN.41: 7 residues within 4Å: Chain L: F.22, Y.23, Y.36, L.48, H.75, W.88 Ligands: HEM.42 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.23

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

HEM.7: 22 residues within 4Å: Chain A: V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: SO4.2, CYN.6 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain H, Hydrophobic interactions: A:Y.36, A:Y.36, A:A.44, A:R.47, A:L.48, A:F.51, A:F.51, A:Y.62, A:L.71, A:L.71, A:R.74, A:F.78, A:F.78, A:I.80, A:I.80, A:W.88, A:W.88, A:W.88, A:Y.115, A:A.120, A:L.123 Hydrogen bonds: A:Y.62, A:Y.62 Salt bridges: A:R.47, A:R.66, A:R.74 pi-Stacking: A:Y.36, A:W.88 Metal complexes: A:H.75 Water bridges: H:E.64 HEM.11: 22 residues within 4Å: Chain B: L.32, V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.10 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:L.32, B:Y.36, B:Y.36, B:A.44, B:R.47, B:L.48, B:F.51, B:F.51, B:Y.62, B:L.71, B:F.78, B:F.78, B:I.80, B:I.80, B:I.80, B:W.88, B:W.88, B:W.88, B:W.88, B:Y.115, B:L.123 Water bridges: B:R.47, B:Y.62 Salt bridges: B:R.47, B:R.66, B:R.74 pi-Stacking: B:Y.36, B:W.88 Metal complexes: B:H.75 HEM.15: 21 residues within 4Å: Chain C: V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.14 29 PLIP interactions: 29 interactions with chain C, Hydrophobic interactions: C:Y.36, C:Y.36, C:A.44, C:R.47, C:L.48, C:F.51, C:Y.62, C:L.71, C:R.74, C:F.78, C:F.78, C:I.80, C:I.80, C:I.80, C:W.88, C:W.88, C:W.88, C:Y.115, C:A.120, C:L.123 Hydrogen bonds: C:Y.62 Water bridges: C:R.47, C:Y.62 Salt bridges: C:R.47, C:R.66, C:R.74 pi-Stacking: C:Y.36, C:W.88 Metal complexes: C:H.75 HEM.18: 22 residues within 4Å: Chain D: V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: SO4.16, CYN.17 29 PLIP interactions: 29 interactions with chain D, Hydrophobic interactions: D:Y.36, D:Y.36, D:A.44, D:R.47, D:L.48, D:F.51, D:Y.62, D:L.71, D:R.74, D:F.78, D:F.78, D:I.80, D:I.80, D:I.80, D:W.88, D:W.88, D:Y.115, D:L.123 Hydrogen bonds: D:Y.62, D:Y.62 Water bridges: D:R.47, D:R.47, D:R.47 Salt bridges: D:R.47, D:R.66, D:R.74 pi-Stacking: D:Y.36, D:W.88 Metal complexes: D:H.75 HEM.22: 21 residues within 4Å: Chain E: V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.21 28 PLIP interactions: 28 interactions with chain E, Hydrophobic interactions: E:Y.36, E:Y.36, E:A.44, E:L.48, E:F.51, E:F.51, E:Y.62, E:L.71, E:R.74, E:F.78, E:F.78, E:I.80, E:I.80, E:I.80, E:W.88, E:W.88, E:W.88, E:Y.115, E:L.123 Hydrogen bonds: E:Y.62, E:Y.62 Water bridges: E:R.47, E:R.47 Salt bridges: E:R.47, E:R.66, E:R.74 pi-Stacking: E:W.88 Metal complexes: E:H.75 HEM.24: 23 residues within 4Å: Chain F: V.35, Y.36, P.37, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.23, SO4.34 27 PLIP interactions: 27 interactions with chain F, Hydrophobic interactions: F:Y.36, F:Y.36, F:A.44, F:L.48, F:F.51, F:F.51, F:L.71, F:R.74, F:F.78, F:F.78, F:I.80, F:I.80, F:I.80, F:E.84, F:W.88, F:W.88, F:Y.115, F:A.120, F:L.123 Water bridges: F:R.47, F:Y.62 Salt bridges: F:R.47, F:R.66, F:R.74 pi-Stacking: F:Y.36, F:W.88 Metal complexes: F:H.75 HEM.28: 25 residues within 4Å: Chain G: L.32, V.35, Y.36, P.37, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, R.85, W.88, Y.115, L.116, A.119, A.120, L.123 Ligands: CYN.27 29 PLIP interactions: 29 interactions with chain G, Hydrophobic interactions: G:L.32, G:Y.36, G:Y.36, G:A.44, G:R.47, G:L.48, G:F.51, G:F.51, G:L.71, G:R.74, G:F.78, G:I.80, G:I.80, G:I.80, G:W.88, G:W.88, G:W.88, G:W.88, G:Y.115, G:L.116, G:L.123 Hydrogen bonds: G:Y.62 Water bridges: G:R.74 Salt bridges: G:R.47, G:R.47, G:R.66, G:R.74 pi-Stacking: G:W.88 Metal complexes: G:H.75 HEM.30: 22 residues within 4Å: Chain H: V.35, Y.36, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, W.88, Y.115, L.116, A.119, A.120, L.123 Ligands: CYN.29 31 PLIP interactions: 31 interactions with chain H, Hydrophobic interactions: H:V.35, H:Y.36, H:A.44, H:R.47, H:L.48, H:F.51, H:F.51, H:L.71, H:R.74, H:F.78, H:F.78, H:I.80, H:I.80, H:E.84, H:W.88, H:W.88, H:W.88, H:W.88, H:Y.115, H:L.116, H:A.119, H:A.120, H:L.123 Hydrogen bonds: H:Y.62 Water bridges: H:R.74 Salt bridges: H:R.47, H:R.47, H:R.66, H:R.74 pi-Stacking: H:W.88 Metal complexes: H:H.75 HEM.33: 24 residues within 4Å: Chain I: L.32, V.35, Y.36, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, R.85, W.88, Y.115, L.116, A.119, A.120, L.123 Ligands: CYN.32 32 PLIP interactions: 32 interactions with chain I, Hydrophobic interactions: I:L.32, I:V.35, I:Y.36, I:Y.36, I:Y.36, I:A.44, I:R.47, I:L.48, I:F.51, I:F.51, I:L.71, I:R.74, I:F.78, I:I.80, I:I.80, I:W.88, I:W.88, I:W.88, I:W.88, I:Y.115, I:L.116, I:L.123 Hydrogen bonds: I:D.40, I:Y.62 Water bridges: I:Y.23, I:R.47, I:R.74 Salt bridges: I:R.47, I:R.66, I:R.74 pi-Stacking: I:W.88 Metal complexes: I:H.75 HEM.37: 22 residues within 4Å: Chain J: V.35, Y.36, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.36 31 PLIP interactions: 31 interactions with chain J, Hydrophobic interactions: J:V.35, J:Y.36, J:Y.36, J:Y.36, J:A.44, J:R.47, J:L.48, J:F.51, J:F.51, J:L.71, J:R.74, J:F.78, J:I.80, J:I.80, J:I.80, J:E.84, J:W.88, J:W.88, J:W.88, J:W.88, J:Y.115, J:L.123 Hydrogen bonds: J:D.40, J:Y.62 Water bridges: J:R.47 Salt bridges: J:R.47, J:R.47, J:R.66, J:R.74 pi-Stacking: J:W.88 Metal complexes: J:H.75 HEM.39: 22 residues within 4Å: Chain K: V.35, Y.36, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, E.84, R.85, W.88, Y.115, A.119, A.120, L.123 Ligands: CYN.38 34 PLIP interactions: 34 interactions with chain K, Hydrophobic interactions: K:Y.36, K:Y.36, K:Y.36, K:A.44, K:R.47, K:L.48, K:F.51, K:F.51, K:L.71, K:L.71, K:R.74, K:F.78, K:F.78, K:I.80, K:I.80, K:W.88, K:W.88, K:W.88, K:W.88, K:Y.115, K:A.120, K:L.123 Hydrogen bonds: K:D.40, K:Y.62 Water bridges: K:Y.23, K:Y.23, K:R.47, K:R.74 Salt bridges: K:R.47, K:R.47, K:R.66, K:R.74 pi-Stacking: K:W.88 Metal complexes: K:H.75 HEM.42: 23 residues within 4Å: Chain L: L.32, V.35, Y.36, D.40, A.44, R.47, L.48, F.51, Y.62, R.66, L.71, R.74, H.75, F.78, I.80, R.85, W.88, Y.115, L.116, A.119, A.120, L.123 Ligands: CYN.41 30 PLIP interactions: 30 interactions with chain L, Hydrophobic interactions: L:L.32, L:V.35, L:Y.36, L:Y.36, L:Y.36, L:A.44, L:L.48, L:F.51, L:F.51, L:L.71, L:L.71, L:R.74, L:F.78, L:F.78, L:I.80, L:I.80, L:W.88, L:W.88, L:W.88, L:W.88, L:Y.115, L:L.116, L:L.123 Water bridges: L:Y.23, L:R.74 Salt bridges: L:R.47, L:R.66, L:R.74 pi-Stacking: L:W.88 Metal complexes: L:H.75

Links

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Citation

Milani, M. et al., A TyrCD1/TrpG8 hydrogen bond network and a TyrB10-TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-05-20

Peptides

Hemoglobin-like protein HbO: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Hemoglobin-like protein HbO