SMTL ID : 7e97.1

Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 58% oxygen saturation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain D: H.91, Q.95 Ligands: OXY.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.45, A:F.46, A:F.46, A:L.73, A:L.90, A:L.99, A:N.103, A:F.104, A:M.107, A:I.138 Hydrogen bonds: A:G.48, D:Q.95 Salt bridges: A:R.65, D:H.91 pi-Stacking: A:H.62 Metal complexes: A:H.94 HEM.3: 19 residues within 4Å: Chain B: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain C: H.93, Q.97 Ligands: OXY.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:L.45, B:F.46, B:L.70, B:L.90, B:I.99, B:I.99, B:F.107, B:F.107, B:V.137 Salt bridges: B:R.48, B:R.65, B:R.97, C:H.93 pi-Stacking: B:H.62 Metal complexes: B:H.94 Hydrogen bonds: C:Q.97 HEM.5: 18 residues within 4Å: Chain B: R.89, Q.93 Chain C: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.6 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:F.50, C:F.50, C:R.69, C:V.70, C:V.70, C:F.109, C:M.112, C:F.136, C:I.143 Salt bridges: C:H.66, C:R.101, B:R.89, B:R.89 pi-Stacking: C:H.66 Metal complexes: C:H.98 Hydrogen bonds: B:Q.93 HEM.7: 18 residues within 4Å: Chain A: H.89, Q.93 Chain D: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.8 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A, Hydrophobic interactions: D:V.45, D:R.67, D:V.68, D:V.107, D:L.110, D:I.141 Hydrogen bonds: D:Q.64, A:Q.93 Metal complexes: D:H.96 Salt bridges: A:H.89, A:H.89 HEM.9: 22 residues within 4Å: Chain E: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain H: H.91, Q.95 Ligands: OXY.10 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain H, Hydrophobic interactions: E:L.45, E:F.46, E:F.46, E:L.73, E:L.90, E:L.99, E:N.103, E:F.104, E:M.107, E:I.138 Hydrogen bonds: E:G.48, H:Q.95 Salt bridges: E:R.65, H:H.91 pi-Stacking: E:H.62 Metal complexes: E:H.94 HEM.11: 19 residues within 4Å: Chain F: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain G: H.93, Q.97 Ligands: OXY.12 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain G, Hydrophobic interactions: F:L.45, F:F.46, F:L.70, F:L.90, F:I.99, F:I.99, F:F.107, F:F.107, F:V.137 Salt bridges: F:R.48, F:R.65, F:R.97, G:H.93 pi-Stacking: F:H.62 Metal complexes: F:H.94 Hydrogen bonds: G:Q.97 HEM.13: 18 residues within 4Å: Chain F: R.89, Q.93 Chain G: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.14 16 PLIP interactions: 13 interactions with chain G, 3 interactions with chain F, Hydrophobic interactions: G:F.50, G:F.50, G:R.69, G:V.70, G:V.70, G:F.109, G:M.112, G:F.136, G:I.143 Salt bridges: G:H.66, G:R.101, F:R.89, F:R.89 pi-Stacking: G:H.66 Metal complexes: G:H.98 Hydrogen bonds: F:Q.93 HEM.15: 18 residues within 4Å: Chain E: H.89, Q.93 Chain H: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.16 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain E, Hydrophobic interactions: H:V.45, H:R.67, H:V.68, H:V.107, H:L.110, H:I.141 Hydrogen bonds: H:Q.64, E:Q.93 Metal complexes: H:H.96 Salt bridges: E:H.89, E:H.89 HEM.17: 22 residues within 4Å: Chain I: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain L: H.91, Q.95 Ligands: OXY.18 16 PLIP interactions: 14 interactions with chain I, 2 interactions with chain L, Hydrophobic interactions: I:L.45, I:F.46, I:F.46, I:L.73, I:L.90, I:L.99, I:N.103, I:F.104, I:M.107, I:I.138 Hydrogen bonds: I:G.48, L:Q.95 Salt bridges: I:R.65, L:H.91 pi-Stacking: I:H.62 Metal complexes: I:H.94 HEM.19: 19 residues within 4Å: Chain J: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain K: H.93, Q.97 Ligands: OXY.20 16 PLIP interactions: 14 interactions with chain J, 2 interactions with chain K, Hydrophobic interactions: J:L.45, J:F.46, J:L.70, J:L.90, J:I.99, J:I.99, J:F.107, J:F.107, J:V.137 Salt bridges: J:R.48, J:R.65, J:R.97, K:H.93 pi-Stacking: J:H.62 Metal complexes: J:H.94 Hydrogen bonds: K:Q.97 HEM.21: 18 residues within 4Å: Chain J: R.89, Q.93 Chain K: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.22 16 PLIP interactions: 13 interactions with chain K, 3 interactions with chain J, Hydrophobic interactions: K:F.50, K:F.50, K:R.69, K:V.70, K:V.70, K:F.109, K:M.112, K:F.136, K:I.143 Salt bridges: K:H.66, K:R.101, J:R.89, J:R.89 pi-Stacking: K:H.66 Metal complexes: K:H.98 Hydrogen bonds: J:Q.93 HEM.23: 18 residues within 4Å: Chain I: H.89, Q.93 Chain L: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.24 11 PLIP interactions: 8 interactions with chain L, 3 interactions with chain I, Hydrophobic interactions: L:V.45, L:R.67, L:V.68, L:V.107, L:L.110, L:I.141 Hydrogen bonds: L:Q.64, I:Q.93 Metal complexes: L:H.96 Salt bridges: I:H.89, I:H.89 HEM.25: 22 residues within 4Å: Chain M: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain P: H.91, Q.95 Ligands: OXY.26 16 PLIP interactions: 14 interactions with chain M, 2 interactions with chain P, Hydrophobic interactions: M:L.45, M:F.46, M:F.46, M:L.73, M:L.90, M:L.99, M:N.103, M:F.104, M:M.107, M:I.138 Hydrogen bonds: M:G.48, P:Q.95 Salt bridges: M:R.65, P:H.91 pi-Stacking: M:H.62 Metal complexes: M:H.94 HEM.27: 19 residues within 4Å: Chain N: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain O: H.93, Q.97 Ligands: OXY.28 16 PLIP interactions: 14 interactions with chain N, 2 interactions with chain O, Hydrophobic interactions: N:L.45, N:F.46, N:L.70, N:L.90, N:I.99, N:I.99, N:F.107, N:F.107, N:V.137 Salt bridges: N:R.48, N:R.65, N:R.97, O:H.93 pi-Stacking: N:H.62 Metal complexes: N:H.94 Hydrogen bonds: O:Q.97 HEM.29: 18 residues within 4Å: Chain N: R.89, Q.93 Chain O: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.30 16 PLIP interactions: 13 interactions with chain O, 3 interactions with chain N, Hydrophobic interactions: O:F.50, O:F.50, O:R.69, O:V.70, O:V.70, O:F.109, O:M.112, O:F.136, O:I.143 Salt bridges: O:H.66, O:R.101, N:R.89, N:R.89 pi-Stacking: O:H.66 Metal complexes: O:H.98 Hydrogen bonds: N:Q.93 HEM.31: 18 residues within 4Å: Chain M: H.89, Q.93 Chain P: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.32 11 PLIP interactions: 8 interactions with chain P, 3 interactions with chain M, Hydrophobic interactions: P:V.45, P:R.67, P:V.68, P:V.107, P:L.110, P:I.141 Hydrogen bonds: P:Q.64, M:Q.93 Metal complexes: P:H.96 Salt bridges: M:H.89, M:H.89 HEM.33: 22 residues within 4Å: Chain Q: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain T: H.91, Q.95 Ligands: OXY.34 16 PLIP interactions: 14 interactions with chain Q, 2 interactions with chain T, Hydrophobic interactions: Q:L.45, Q:F.46, Q:F.46, Q:L.73, Q:L.90, Q:L.99, Q:N.103, Q:F.104, Q:M.107, Q:I.138 Hydrogen bonds: Q:G.48, T:Q.95 Salt bridges: Q:R.65, T:H.91 pi-Stacking: Q:H.62 Metal complexes: Q:H.94 HEM.35: 19 residues within 4Å: Chain R: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain S: H.93, Q.97 Ligands: OXY.36 16 PLIP interactions: 2 interactions with chain S, 14 interactions with chain R, Hydrogen bonds: S:Q.97 Salt bridges: S:H.93, R:R.48, R:R.65, R:R.97 Hydrophobic interactions: R:L.45, R:F.46, R:L.70, R:L.90, R:I.99, R:I.99, R:F.107, R:F.107, R:V.137 pi-Stacking: R:H.62 Metal complexes: R:H.94 HEM.37: 18 residues within 4Å: Chain R: R.89, Q.93 Chain S: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.38 16 PLIP interactions: 13 interactions with chain S, 3 interactions with chain R, Hydrophobic interactions: S:F.50, S:F.50, S:R.69, S:V.70, S:V.70, S:F.109, S:M.112, S:F.136, S:I.143 Salt bridges: S:H.66, S:R.101, R:R.89, R:R.89 pi-Stacking: S:H.66 Metal complexes: S:H.98 Hydrogen bonds: R:Q.93 HEM.39: 18 residues within 4Å: Chain Q: H.89, Q.93 Chain T: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.40 11 PLIP interactions: 8 interactions with chain T, 3 interactions with chain Q, Hydrophobic interactions: T:V.45, T:R.67, T:V.68, T:V.107, T:L.110, T:I.141 Hydrogen bonds: T:Q.64, Q:Q.93 Metal complexes: T:H.96 Salt bridges: Q:H.89, Q:H.89 HEM.41: 22 residues within 4Å: Chain U: L.45, F.46, G.48, V.49, H.62, R.65, V.66, A.69, L.70, L.73, L.90, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain X: H.91, Q.95 Ligands: OXY.42 16 PLIP interactions: 14 interactions with chain U, 2 interactions with chain X, Hydrophobic interactions: U:L.45, U:F.46, U:F.46, U:L.73, U:L.90, U:L.99, U:N.103, U:F.104, U:M.107, U:I.138 Hydrogen bonds: U:G.48, X:Q.95 Salt bridges: U:R.65, X:H.91 pi-Stacking: U:H.62 Metal complexes: U:H.94 HEM.43: 19 residues within 4Å: Chain V: L.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, H.94, R.97, I.99, G.103, F.107, V.137 Chain W: H.93, Q.97 Ligands: OXY.44 16 PLIP interactions: 14 interactions with chain V, 2 interactions with chain W, Hydrophobic interactions: V:L.45, V:F.46, V:L.70, V:L.90, V:I.99, V:I.99, V:F.107, V:F.107, V:V.137 Salt bridges: V:R.48, V:R.65, V:R.97, W:H.93 pi-Stacking: V:H.62 Metal complexes: V:H.94 Hydrogen bonds: W:Q.97 HEM.45: 18 residues within 4Å: Chain V: R.89, Q.93 Chain W: L.49, F.50, V.53, H.66, R.69, V.70, L.74, Q.97, H.98, R.101, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.46 16 PLIP interactions: 3 interactions with chain V, 13 interactions with chain W, Hydrogen bonds: V:Q.93 Salt bridges: V:R.89, V:R.89, W:H.66, W:R.101 Hydrophobic interactions: W:F.50, W:F.50, W:R.69, W:V.70, W:V.70, W:F.109, W:M.112, W:F.136, W:I.143 pi-Stacking: W:H.66 Metal complexes: W:H.98 HEM.47: 18 residues within 4Å: Chain U: H.89, Q.93 Chain X: F.39, V.45, M.49, F.50, Q.64, R.67, V.68, A.72, L.92, H.96, V.102, A.106, V.107, L.110, I.141 Ligands: OXY.48 11 PLIP interactions: 8 interactions with chain X, 3 interactions with chain U, Hydrophobic interactions: X:V.45, X:R.67, X:V.68, X:V.107, X:L.110, X:I.141 Hydrogen bonds: X:Q.64, U:Q.93 Metal complexes: X:H.96 Salt bridges: U:H.89, U:H.89

24 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 6 residues within 4Å: Chain A: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) OXY.4: 6 residues within 4Å: Chain B: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) OXY.6: 6 residues within 4Å: Chain C: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.66 OXY.8: 5 residues within 4Å: Chain D: F.50, V.68, H.96, L.110 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) OXY.10: 6 residues within 4Å: Chain E: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) OXY.12: 6 residues within 4Å: Chain F: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.11 No protein-ligand interaction detected (PLIP) OXY.14: 6 residues within 4Å: Chain G: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.66 OXY.16: 5 residues within 4Å: Chain H: F.50, V.68, H.96, L.110 Ligands: HEM.15 No protein-ligand interaction detected (PLIP) OXY.18: 6 residues within 4Å: Chain I: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.17 No protein-ligand interaction detected (PLIP) OXY.20: 6 residues within 4Å: Chain J: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.19 No protein-ligand interaction detected (PLIP) OXY.22: 6 residues within 4Å: Chain K: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.21 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.66 OXY.24: 5 residues within 4Å: Chain L: F.50, V.68, H.96, L.110 Ligands: HEM.23 No protein-ligand interaction detected (PLIP) OXY.26: 6 residues within 4Å: Chain M: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.25 No protein-ligand interaction detected (PLIP) OXY.28: 6 residues within 4Å: Chain N: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.27 No protein-ligand interaction detected (PLIP) OXY.30: 6 residues within 4Å: Chain O: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.29 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:H.66 OXY.32: 5 residues within 4Å: Chain P: F.50, V.68, H.96, L.110 Ligands: HEM.31 No protein-ligand interaction detected (PLIP) OXY.34: 6 residues within 4Å: Chain Q: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.33 No protein-ligand interaction detected (PLIP) OXY.36: 6 residues within 4Å: Chain R: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.35 No protein-ligand interaction detected (PLIP) OXY.38: 6 residues within 4Å: Chain S: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.37 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:H.66 OXY.40: 5 residues within 4Å: Chain T: F.50, V.68, H.96, L.110 Ligands: HEM.39 No protein-ligand interaction detected (PLIP) OXY.42: 6 residues within 4Å: Chain U: F.32, F.46, H.62, V.66, H.94 Ligands: HEM.41 No protein-ligand interaction detected (PLIP) OXY.44: 6 residues within 4Å: Chain V: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.43 No protein-ligand interaction detected (PLIP) OXY.46: 6 residues within 4Å: Chain W: F.36, F.50, H.66, V.70, H.98 Ligands: HEM.45 No protein-ligand interaction detected (PLIP) OXY.48: 5 residues within 4Å: Chain X: F.50, V.68, H.96, L.110 Ligands: HEM.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numoto, N. et al., Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj (2021)

Release Date

2021-10-06

Peptides

Extracellular giant hemoglobin major globin subunit A1: AEIMQU
Extracellular giant hemoglobin major globin subunit A2: BFJNRV
Extracellular giant hemoglobin major globin subunit B2: CGKOSW
Giant hemoglobin B1b globin chain: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

Extracellular giant hemoglobin major globin subunit A1

Extracellular giant hemoglobin major globin subunit A2

Extracellular giant hemoglobin major globin subunit B2

Giant hemoglobin B1b globin chain

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