1YHU

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.243

Literature

Macromolecules
Sequence Display for 1YHU

Classification: OXYGEN STORAGE / TRANSPORT

Total Structure Weight: 396753.97

Macromolecule Entities
Molecule Chains Length Organism Details
hemoglobin A1 chain A, E, I..., M, Q, UA, E, I, M, Q, U 145 Riftia pachyptila Gene Name(s): hbA1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Giant hemoglobins B chain B, F, J..., N, R, VB, F, J, N, R, V 144 Riftia pachyptila Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
hemoglobin B1a chain C, G, K..., O, S, WC, G, K, O, S, W 148 Riftia pachyptila Mutation: Q17E, S20W, P22A, D23A, R27A, K29R, L30V, C32A, H34E, A35E, E39A, E58D, N65Q, M69V, Y81A, K107G, G111Q, A112L, K119E, M121L
Gene Name(s): hbB1a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
hemoglobin B2 chain D, H, L..., P, T, XD, H, L, P, T, X 149 Riftia pachyptila Gene Name(s): hbB2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B, F, J, N, R, V ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXY
Query on OXY

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.243
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 195.84 α = 90.00
b = 195.84 β = 90.00
c = 308.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-10
  • Released Date: 2005-02-08
  • Deposition author(s): Flores, J.F., Fisher, C.R., Carney, S.L., Green, B.N., Freytag, J.K., Schaeffer, S.W., Royer, W.E.

Revision History

  • Version 1_0: 2005-02-08

    Type: Initial release

  • Version 1_1: 2008-04-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance

  • Version 1_3: 2013-03-06

    Type: Data collection