SMTL ID : 3mvc.1 (1 other biounit)

High resolution crystal structure of the heme domain of GLB-6 from C. elegans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: F.31, I.41, M.44, I.45, R.56, H.60, L.63, F.64, L.67, K.91, H.92, W.94, Y.100, F.104, L.109, F.112, L.148 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.31, A:M.44, A:F.64, A:L.67, A:K.91, A:W.94, A:W.94, A:Y.100, A:Y.100, A:Y.100, A:L.109, A:F.112, A:L.148 Salt bridges: A:R.56 pi-Stacking: A:F.104 Metal complexes: A:H.60, A:H.92

3 x PR: PRASEODYMIUM ION(Non-covalent)

PR.2: 3 residues within 4Å: Chain A: E.90, E.155 Ligands: PR.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.90, A:E.90, A:E.155, H2O.1 PR.3: 3 residues within 4Å: Chain A: P.95, R.161 Ligands: NO3.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.95, A:R.161, H2O.1, H2O.1, H2O.1 PR.4: 3 residues within 4Å: Chain A: E.87, E.90 Ligands: PR.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.87, A:E.87, A:E.90, H2O.1

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 5 residues within 4Å: Chain A: P.95, T.96, R.97, R.161 Ligands: PR.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97 Water bridges: A:N.98 NO3.6: 5 residues within 4Å: Chain A: T.4, P.6, Q.7, T.132, T.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.4 Water bridges: A:T.130 NO3.7: 5 residues within 4Å: Chain A: R.12, W.15, N.16, I.72, A.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16 Water bridges: A:A.73, A:A.73 NO3.8: 1 residues within 4Å: Chain A: H.107 No protein-ligand interaction detected (PLIP) NO3.9: 3 residues within 4Å: Chain A: Q.7, R.135, K.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.7, A:R.135, A:R.135, A:K.139 NO3.10: 5 residues within 4Å: Chain A: R.32, R.42, M.46, H.54, L.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:R.42 Water bridges: A:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, J. et al., Structure and properties of a bis-histidyl ligated globin from Caenorhabditis elegans. Biochemistry (2010)

Release Date

2010-06-16

Peptides

Globin protein 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Globin protein 6

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