SMTL ID : 4b3w.1

Crystal structure of human cytoglobin H(E7)Q mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: F.49, A.56, Y.59, F.60, Q.81, R.84, V.85, A.88, L.89, V.109, A.112, H.113, H.117, V.119, Y.123, F.124, L.127 Ligands: CYN.2 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.49, A:Y.59, A:F.60, A:F.60, A:F.60, A:R.84, A:V.85, A:L.89, A:V.109, A:V.119, A:V.119, A:Y.123, A:F.124 Water bridges: A:H.113 Salt bridges: A:H.117 pi-Stacking: A:H.117, A:F.124 Metal complexes: A:H.113 HEM.4: 15 residues within 4Å: Chain B: A.56, Y.59, F.60, Q.62, Q.81, R.84, V.85, A.88, H.113, H.117, V.119, Y.123, F.124, L.127 Ligands: CYN.5 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:Y.59, B:Y.59, B:F.60, B:F.60, B:F.60, B:F.60, B:R.84, B:V.85, B:A.88, B:V.119, B:V.119, B:F.124 Hydrogen bonds: B:Q.62, B:Q.81 Salt bridges: B:H.113, B:H.117 pi-Stacking: B:H.117 pi-Cation interactions: B:H.113 Metal complexes: B:H.113

2 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 4 residues within 4Å: Chain A: F.60, Q.81, V.85 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.81 CYN.5: 3 residues within 4Å: Chain B: Q.81, V.85 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.81

2 x FC6: HEXACYANOFERRATE(3-)(Non-covalent)

FC6.3: 7 residues within 4Å: Chain A: K.125, R.155, G.156, Y.159 Chain B: F.53, P.54, S.55 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.55, A:K.125, A:R.155 FC6.6: 7 residues within 4Å: Chain A: F.53, P.54, S.55 Chain B: K.125, R.155, G.156, Y.159 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.125, B:R.155, A:S.55, A:S.55

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

ACT.7: 2 residues within 4Å: Chain B: P.76, Q.77 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabba, M. et al., Co Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin. Plos One (2013)

Release Date

2013-01-23

Peptides

CYTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOGLOBIN