SMTL ID : 3wfx.1

Crystal Structure of the Imidazole-Bound Form of the HGbRL's Globin Domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: L.77, R.80, H.81, Y.84, V.86, H.90, Y.91, V.94, Y.122, L.125, M.129 Chain B: L.41, F.42, K.43, D.55, V.56, W.59, I.60 Ligands: IMD.5, HEZ.10 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:Y.84, A:Y.84, A:V.86, A:V.86, A:Y.91, A:V.94, A:Y.122, A:L.125, A:L.125, B:L.41, B:L.41, B:F.42, B:F.42, B:V.56, B:I.60 Hydrogen bonds: A:Y.84, A:Y.84, B:K.43 Salt bridges: A:R.80, A:H.81 Metal complexes: A:H.81 HEM.7: 20 residues within 4Å: Chain A: L.41, F.42, K.43, I.44, D.55, V.56, W.59, I.60 Chain B: L.77, R.80, H.81, Y.84, V.86, H.90, Y.91, V.94, Y.122, L.125, M.129 Ligands: IMD.4 23 PLIP interactions: 10 interactions with chain A, 13 interactions with chain B, Hydrophobic interactions: A:L.41, A:F.42, A:F.42, A:F.42, A:F.42, A:I.44, A:V.56, A:V.56, A:I.60, B:L.77, B:L.77, B:Y.84, B:Y.84, B:H.90, B:Y.91, B:Y.91, B:V.94, B:Y.122 Hydrogen bonds: A:K.43, B:Y.84 Salt bridges: B:R.80, B:H.81 Metal complexes: B:H.81

6 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.2: 9 residues within 4Å: Chain A: I.60, N.63, L.64, I.67 Chain B: L.71, A.74, A.121, L.125, V.128 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.67, B:L.125 Hydrogen bonds: A:I.60, A:N.63, A:N.63 HEZ.3: 8 residues within 4Å: Chain A: Y.91, P.92, H.96, I.99, T.119, Y.122, E.123, A.126 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.123 HEZ.6: 3 residues within 4Å: Chain A: P.92, H.96 Chain B: R.30 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.30 Hydrophobic interactions: A:H.96 Water bridges: A:H.96, A:R.103 HEZ.8: 8 residues within 4Å: Chain B: P.92, G.95, H.96, I.99, E.115, T.119, Y.122, E.123 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.99, B:T.119, B:Y.122, B:E.123 Hydrogen bonds: B:E.115, B:E.115 Water bridges: B:R.103 HEZ.9: 9 residues within 4Å: Chain A: A.74, A.121, A.124, L.125, V.128 Chain B: I.60, N.63, L.64, I.67 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.67, A:A.124, A:L.125 Hydrogen bonds: B:I.60, B:N.63 Water bridges: B:N.63, A:L.71 HEZ.10: 6 residues within 4Å: Chain B: D.55, N.58, W.59, L.62, N.63 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.59, B:L.62 Hydrogen bonds: B:D.55 Water bridges: B:N.63, B:D.66

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: F.27, F.42, V.56 Chain B: V.94 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) IMD.5: 5 residues within 4Å: Chain B: F.27, Y.28, F.42, V.56 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teh, A.H. et al., Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites. Sci Rep (2015)

Release Date

2014-08-06

Peptides

Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain

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