- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.45 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.1: 19 residues within 4Å:- Chain A: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136
- Ligands: CMO.2
21 PLIP interactions:21 interactions with chain A,- Hydrophobic interactions: A:Y.42, A:F.43, A:K.61, A:A.65, A:L.83, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:L.101, A:V.132, A:L.136
- Water bridges: A:K.61, A:K.61
- Salt bridges: A:H.45, A:K.61
- pi-Stacking: A:H.58
- Metal complexes: A:H.87
HEM.8: 17 residues within 4Å:- Chain C: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136
- Ligands: CMO.9
18 PLIP interactions:18 interactions with chain C,- Hydrophobic interactions: C:Y.42, C:F.43, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:V.93, C:N.97, C:F.98, C:L.101, C:L.136
- Water bridges: C:K.61, C:K.61
- Salt bridges: C:H.45, C:K.61
- pi-Stacking: C:H.58
- Metal complexes: C:H.87
- 8 x CMO: CARBON MONOXIDE(Non-functional Binders)
CMO.2: 5 residues within 4Å:- Chain A: L.29, H.58, V.62, L.101
- Ligands: HEM.1
No protein-ligand interaction detected (PLIP)CMO.3: 6 residues within 4Å:- Chain A: W.14, A.21, Y.24, G.25, A.63, L.105
No protein-ligand interaction detected (PLIP)CMO.5: 6 residues within 4Å:- Chain B: F.103, G.107, V.134, V.137, A.138
- Ligands: HNI.4
No protein-ligand interaction detected (PLIP)CMO.6: 7 residues within 4Å:- Chain B: G.24, A.27, L.28, G.64, V.67, L.68, L.106
No protein-ligand interaction detected (PLIP)CMO.9: 6 residues within 4Å:- Chain C: L.29, F.43, H.58, V.62, L.101
- Ligands: HEM.8
No protein-ligand interaction detected (PLIP)CMO.10: 6 residues within 4Å:- Chain C: W.14, A.21, Y.24, G.25, A.63, L.105
No protein-ligand interaction detected (PLIP)CMO.12: 6 residues within 4Å:- Chain D: F.103, G.107, V.134, V.137, A.138
- Ligands: HNI.11
1 PLIP interactions:1 interactions with chain D- Water bridges: D:G.107
CMO.13: 7 residues within 4Å:- Chain D: G.24, A.27, L.28, G.64, V.67, L.68, L.106
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:L.28
- 2 x HNI: PROTOPORPHYRIN IX CONTAINING NI(II)(Non-covalent)
HNI.4: 18 residues within 4Å:- Chain B: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141
- Ligands: CMO.5
20 PLIP interactions:20 interactions with chain B,- Hydrophobic interactions: B:L.31, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:K.66, B:V.67, B:F.71, B:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:F.103, B:L.106, B:L.141
- Salt bridges: B:K.66
- pi-Stacking: B:H.63
- Metal complexes: B:H.92
HNI.11: 18 residues within 4Å:- Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141
- Ligands: CMO.12
20 PLIP interactions:20 interactions with chain D,- Hydrophobic interactions: D:L.31, D:F.41, D:F.41, D:F.42, D:F.42, D:F.42, D:K.66, D:V.67, D:A.70, D:L.88, D:L.91, D:L.96, D:L.96, D:V.98, D:V.98, D:L.106, D:L.141
- Water bridges: D:H.63
- pi-Stacking: D:H.63
- Metal complexes: D:H.92
- 1 x 2FU: BUT-2-ENEDIAL(Covalent)
2FU.7: 3 residues within 4Å:- Chain B: V.1, K.82
- Chain D: K.82
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain D- Hydrophobic interactions: B:V.1
- Water bridges: D:V.1
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shibayama, N. et al., Direct observation of ligand migration within human hemoglobin at work. Proc.Natl.Acad.Sci.USA (2020)
- Release Date
- 2020-02-19
- Peptides
- Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EC
GB
FD
H
SMTL ID : 6kae.2 (1 other biounit)
Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K: Light
Hemoglobin subunit alpha
Toggle Identical (AC)Hemoglobin subunit beta
Toggle Identical (BD)Related Entries With Identical Sequence
1a00.1 | 1a01.1 | 1a0u.1 | 1a0z.1 | 1a3n.1 | 1a3o.1 | 1a9w.1 | 1aj9.1 | 1b86.1 | 1bab.1 | 1bbb.1 | 1bij.1 | 1buw.1 | 1bz0.1 | 1bz1.1 | 1bzz.1 | 1cbl.1 | 1cbm.1 | 1cls.1 | 1cmy.1 | 1coh.1 | 1dke.1 | 1dxt.1 | 1dxu.1 | 1dxv.1 | 1fdh.1 | 1fn3.1 | 1g9v.1 | 1gbu.1 | 1gbv.1 more...less...1gzx.1 | 1hab.1 | 1hac.1 | 1hba.1 | 1hbb.1 | 1hbs.1 | 1hbs.2 | 1hco.1 | 1hdb.1 | 1hga.1 | 1hgb.1 | 1hgc.1 | 1hho.1 | 1ird.1 | 1j3y.1 | 1j3y.2 | 1j3z.1 | 1j3z.2 | 1j40.1 | 1j40.2 | 1j41.1 | 1j41.2 | 1jy7.1 | 1jy7.2 | 1jy7.3 | 1k0y.1 | 1k1k.1 | 1kd2.1 | 1lfl.1 | 1lfl.2 | 1lfq.1 | 1lft.1 | 1lfv.1 | 1lfy.1 | 1lfz.1 | 1ljw.1 | 1m9p.1 | 1mko.1 | 1nej.1 | 1nih.1 | 1nqp.1 | 1qsh.1 | 1qsi.1 | 1qxd.1 | 1qxd.2 | 1qxe.1 | 1qxe.2 | 1qxe.3 | 1r1x.1 | 1r1y.1 | 1rps.1 | 1rq3.1 | 1rq4.1 | 1rqa.1 | 1rvw.1 | 1sdk.1 | 1sdk.2 | 1sdl.1 | 1sdl.2 | 1shr.1 | 1si4.1 | 1thb.1 | 1uiw.1 | 1uiw.2 | 1vwt.1 | 1xxt.1 | 1xy0.1 | 1xye.1 | 1xz2.1 | 1xz4.1 | 1xz5.1 | 1xz7.1 | 1xzu.1 | 1xzv.1 | 1y09.1 | 1y0a.1 | 1y0c.1 | 1y0d.1 | 1y0t.1 | 1y0w.1 | 1y22.1 | 1y2z.1 | 1y31.1 | 1y35.1 | 1y45.1 | 1y46.1 | 1y4b.1 | 1y4f.1 | 1y4g.1 | 1y4p.1 | 1y4q.1 | 1y4r.1 | 1y4v.1 | 1y5f.1 | 1y5j.1 | 1y5k.1 | 1y7c.1 | 1y7d.1 | 1y7g.1 | 1y7z.1 | 1y83.1 | 1y85.1 | 1y8w.1 | 1ydz.1 | 1ye0.1 | 1ye1.1 | 1ye2.1 | 1yen.1 | 1yeo.1 | 1yeq.1 | 1yeu.1 | 1yev.1 | 1yff.1 | 1yff.2 | 1yg5.1 | 1ygd.1 | 1ygf.1 | 1yh9.1 | 1yhe.1 | 1yhr.1 | 1yie.1 | 1yih.1 | 1yvq.1 | 1yvt.1 | 1yzi.1 | 2d5z.1 | 2d60.1 | 2dn1.1 | 2dn2.1 | 2dn3.1 | 2dxm.1 | 2h35.1 | 2hbc.1 | 2hbd.1 | 2hbe.1 | 2hbf.1 | 2hbs.1 | 2hbs.2 | 2hco.1 | 2hhb.1 | 2hhd.1 | 2hhe.1 | 2m6z.1 | 2w6v.1 | 2yrs.1 | 2yrs.2 | 3b75.1 | 3b75.2 | 3b75.3 | 3d17.1 | 3d7o.1 | 3dut.1 | 3hhb.1 | 3hxn.1 | 3ic0.1 | 3ic2.1 | 3kmf.1 | 3nl7.1 | 3nmm.1 | 3odq.1 | 3onz.1 | 3oo4.1 | 3oo5.1 | 3ovu.1 | 3p5q.1 | 3qjb.1 | 3qjc.1 | 3qjd.1 | 3qje.1 | 3r5i.1 | 3s48.1 | 3s48.2 | 3s65.1 | 3s66.1 | 3szk.1 | 3szk.2 | 3wcp.1 | 3whm.1 | 4fc3.1 | 4hhb.1 | 4ij2.1 | 4l7y.1 | 4m4a.1 | 4m4b.1 | 4mqc.1 | 4mqg.1 | 4mqh.1 | 4mqj.1 | 4mqj.2 | 4mqk.1 | 4mqk.2 | 4n7n.1 | 4n7n.2 | 4n7n.3 | 4n7o.1 | 4n7o.2 | 4n7o.3 | 4n7p.1 | 4n7p.2 | 4n7p.3 | 4n8t.1 | 4ni0.1 | 4ni1.1 | 4rol.1 | 4rom.1 | 4wjg.1 | 4wjg.2 | 4wjg.3 | 4x0l.1 | 4xs0.1 | 5e29.1 | 5e6e.1 | 5e83.1 | 5ee4.1 | 5ee4.2 | 5hu6.1 | 5hy8.1 | 5hy8.2 | 5hy8.3 | 5jdo.1 | 5kdq.1 | 5ksi.1 | 5ksj.1 | 5ni1.1 | 5u3i.1 | 5ucu.1 | 5ufj.1 | 5urc.1 | 5vmm.1 | 5wog.1 | 5woh.1 | 5x2r.1 | 5x2r.2 | 5x2r.3 | 5x2s.1 | 5x2s.2 | 5x2s.3 | 5x2t.1 | 5x2t.2 | 5x2t.3 | 5x2u.1 | 5x2u.2 | 5x2u.3 | 6bnr.1 | 6bwp.1 | 6bwu.1 | 6di4.1 | 6fqf.1 | 6hbw.1 | 6hk2.1 | 6ka9.1 | 6ka9.2 | 6kae.1 | 6kah.1 | 6kah.2 | 6kai.1 | 6kai.2 | 6kao.1 | 6kap.1 | 6kaq.1 | 6kar.1 | 6kas.1 | 6kat.1 | 6kau.1 | 6kav.1 | 6l5v.1 | 6l5w.1 | 6l5x.1 | 6l5y.1 | 6lcw.1 | 6lcw.2 | 6lcx.1 | 6lcx.2 | 6nq5.1 | 6tb2.1 | 6xd9.1 | 6xdt.1 | 6xe7.1 | 7dy3.1 | 7dy3.2 | 7dy4.1 | 7dy4.2 | 7jjq.1 | 7jxz.1 | 7jy0.1 | 7jy1.1 | 7jy3.1 | 7pcf.1 | 7pch.1 | 7pcq.1 | 7uvb.1 | 8dov.1 | 8dov.2 | 8fdk.1 | 8fdl.1 | 8fdm.1 | 8fdn.1