SMTL ID : 7vlf.1

Oxy-deoxy intermediate of V2 hemoglobin at 26% oxygen saturation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: D.81 Chain D: N.58, S.60 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.81, D:N.58 NAG-FUC.2: 2 residues within 4Å: Chain E: D.81 Chain H: N.58 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:D.81, H:N.58 NAG-FUC.17: 3 residues within 4Å: Chain I: D.81 Chain L: N.58, S.60 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:D.81, L:N.58 NAG-FUC.18: 2 residues within 4Å: Chain M: D.81 Chain P: N.58 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:D.81, P:N.58 NAG-FUC.33: 3 residues within 4Å: Chain Q: D.81 Chain T: N.58, S.60 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain T Hydrogen bonds: Q:D.81, T:N.58 NAG-FUC.34: 2 residues within 4Å: Chain U: D.81 Chain X: N.58 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain X Hydrogen bonds: U:D.81, X:N.58

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

HEM.3: 19 residues within 4Å: Chain A: L.45, F.46, S.48, V.49, H.62, R.65, V.66, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain D: H.94, Q.98 Ligands: HEM.8 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.45, A:F.46, A:F.46, A:V.49, A:L.70, A:L.99, A:N.103, A:F.104, A:F.104, A:F.104, A:F.107, A:F.107, A:I.135, A:I.139 Hydrogen bonds: A:S.48, D:Q.98 Water bridges: A:S.48 Salt bridges: A:R.65, D:H.94 pi-Stacking: A:H.62 Metal complexes: A:H.94 HEM.4: 18 residues within 4Å: Chain B: M.46, F.47, R.49, V.50, H.63, R.66, V.67, L.71, L.91, Q.94, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain C: H.94 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.47, B:V.67, B:L.91, B:V.100, B:Q.104, B:Y.105, B:V.108, B:I.141 Hydrogen bonds: B:R.49, B:V.50, B:R.98 Salt bridges: B:R.49, C:H.94 Metal complexes: B:H.95 HEM.6: 20 residues within 4Å: Chain B: H.90, Q.94 Chain C: L.50, F.51, R.53, V.54, H.67, R.70, V.71, L.75, Q.98, H.99, R.102, V.105, G.109, F.110, I.113, T.141, M.144 Ligands: OXY.7 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:L.50, C:F.51, C:F.51, C:V.71, C:L.75, C:R.102, C:F.110, C:F.110, C:I.113, C:T.141 Hydrogen bonds: C:Q.98, B:Q.94 Water bridges: C:R.53 Salt bridges: C:R.53, C:H.67, C:R.70, C:R.102, B:H.90 Metal complexes: C:H.99 HEM.8: 17 residues within 4Å: Chain A: H.89, Q.93 Chain D: F.51, N.53, V.54, H.67, R.70, V.71, Q.98, H.99, R.102, L.105, Y.109, F.110, M.113 Ligands: HEM.3, OXY.9 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: D:F.51, D:F.51, D:V.71, D:L.105, D:L.105, D:Y.109, D:F.110, D:F.110, D:F.110, D:F.110, D:M.113 Hydrogen bonds: D:N.53, A:Q.93 Salt bridges: D:R.102, A:H.89 pi-Stacking: D:H.67 Metal complexes: D:H.99 HEM.10: 18 residues within 4Å: Chain E: L.45, F.46, S.48, H.62, R.65, G.69, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain H: H.94, Q.98 Ligands: HEM.16 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain H, Hydrophobic interactions: E:F.46, E:F.46, E:L.70, E:L.99, E:N.103, E:F.104, E:F.104, E:F.104, E:F.107, E:F.107, E:F.107, E:I.135, E:I.139 Hydrogen bonds: E:R.65, H:Q.98 Salt bridges: E:R.65, H:H.94, H:H.94 pi-Stacking: E:H.62 Metal complexes: E:H.94 HEM.11: 19 residues within 4Å: Chain F: M.46, F.47, R.49, V.50, H.63, R.66, V.67, G.70, L.71, L.91, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain G: H.94 Ligands: OXY.12 16 PLIP interactions: 1 interactions with chain G, 15 interactions with chain F, Salt bridges: G:H.94, F:R.98 Hydrophobic interactions: F:F.47, F:F.47, F:L.71, F:L.71, F:L.91, F:L.91, F:Q.104, F:Y.105, F:Y.105, F:V.108, F:I.141 Hydrogen bonds: F:R.98 pi-Stacking: F:H.63 Metal complexes: F:H.95 HEM.14: 18 residues within 4Å: Chain F: H.90 Chain G: L.50, F.51, R.53, V.54, H.67, R.70, V.71, G.74, L.75, Q.98, H.99, R.102, G.109, F.110, I.113, M.144 Ligands: OXY.15 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain F, Hydrophobic interactions: G:L.50, G:F.51, G:F.110, G:F.110, G:I.113 Hydrogen bonds: G:V.54, G:Q.98 Salt bridges: G:R.53, G:R.102, F:H.90 pi-Stacking: G:H.67 Metal complexes: G:H.99 HEM.16: 19 residues within 4Å: Chain E: H.89, Q.93 Chain H: S.47, L.50, F.51, N.53, V.54, H.67, R.70, V.71, L.75, L.95, Q.98, H.99, R.102, Y.109, F.110, M.113 Ligands: HEM.10 13 PLIP interactions: 2 interactions with chain E, 11 interactions with chain H, Hydrogen bonds: E:Q.93, H:V.54 Salt bridges: E:H.89, H:R.102 Hydrophobic interactions: H:F.51, H:F.51, H:L.95, H:Y.109, H:F.110, H:F.110, H:M.113 pi-Stacking: H:H.67 Metal complexes: H:H.99 HEM.19: 19 residues within 4Å: Chain I: L.45, F.46, S.48, V.49, H.62, R.65, V.66, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain L: H.94, Q.98 Ligands: HEM.24 20 PLIP interactions: 18 interactions with chain I, 2 interactions with chain L, Hydrophobic interactions: I:L.45, I:F.46, I:F.46, I:V.49, I:L.99, I:N.103, I:F.104, I:F.104, I:F.104, I:F.107, I:F.107, I:I.135, I:I.139 Hydrogen bonds: I:S.48, L:Q.98 Water bridges: I:S.48 Salt bridges: I:R.65, L:H.94 pi-Stacking: I:H.62 Metal complexes: I:H.94 HEM.20: 18 residues within 4Å: Chain J: M.46, F.47, R.49, V.50, H.63, R.66, V.67, L.71, L.91, Q.94, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain K: H.94 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain K, Hydrophobic interactions: J:F.47, J:V.67, J:L.91, J:V.100, J:Q.104, J:Y.105, J:V.108, J:I.141 Hydrogen bonds: J:R.49, J:V.50, J:R.98 Salt bridges: J:R.49, K:H.94 Metal complexes: J:H.95 HEM.22: 20 residues within 4Å: Chain J: H.90, Q.94 Chain K: L.50, F.51, R.53, V.54, H.67, R.70, V.71, L.75, Q.98, H.99, R.102, V.105, G.109, F.110, I.113, T.141, M.144 Ligands: OXY.23 19 PLIP interactions: 17 interactions with chain K, 2 interactions with chain J, Hydrophobic interactions: K:L.50, K:F.51, K:F.51, K:V.71, K:L.75, K:R.102, K:F.110, K:F.110, K:I.113, K:T.141 Hydrogen bonds: K:Q.98, J:Q.94 Water bridges: K:R.53 Salt bridges: K:R.53, K:H.67, K:R.70, K:R.102, J:H.90 Metal complexes: K:H.99 HEM.24: 17 residues within 4Å: Chain I: H.89, Q.93 Chain L: F.51, N.53, V.54, H.67, R.70, V.71, Q.98, H.99, R.102, L.105, Y.109, F.110, M.113 Ligands: HEM.19, OXY.25 17 PLIP interactions: 15 interactions with chain L, 2 interactions with chain I, Hydrophobic interactions: L:F.51, L:F.51, L:V.71, L:L.105, L:L.105, L:Y.109, L:F.110, L:F.110, L:F.110, L:F.110, L:M.113 Hydrogen bonds: L:N.53, I:Q.93 Salt bridges: L:R.102, I:H.89 pi-Stacking: L:H.67 Metal complexes: L:H.99 HEM.26: 18 residues within 4Å: Chain M: L.45, F.46, S.48, H.62, R.65, G.69, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain P: H.94, Q.98 Ligands: HEM.32 20 PLIP interactions: 3 interactions with chain P, 17 interactions with chain M, Hydrogen bonds: P:Q.98, M:R.65 Salt bridges: P:H.94, P:H.94, M:R.65 Hydrophobic interactions: M:F.46, M:F.46, M:L.70, M:L.99, M:N.103, M:F.104, M:F.104, M:F.104, M:F.107, M:F.107, M:F.107, M:I.135, M:I.139 pi-Stacking: M:H.62 Metal complexes: M:H.94 HEM.27: 19 residues within 4Å: Chain N: M.46, F.47, R.49, V.50, H.63, R.66, V.67, G.70, L.71, L.91, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain O: H.94 Ligands: OXY.28 16 PLIP interactions: 15 interactions with chain N, 1 interactions with chain O, Hydrophobic interactions: N:F.47, N:F.47, N:L.71, N:L.71, N:L.91, N:L.91, N:Q.104, N:Y.105, N:Y.105, N:V.108, N:I.141 Hydrogen bonds: N:R.98 Salt bridges: N:R.98, O:H.94 pi-Stacking: N:H.63 Metal complexes: N:H.95 HEM.30: 18 residues within 4Å: Chain N: H.90 Chain O: L.50, F.51, R.53, V.54, H.67, R.70, V.71, G.74, L.75, Q.98, H.99, R.102, G.109, F.110, I.113, M.144 Ligands: OXY.31 12 PLIP interactions: 11 interactions with chain O, 1 interactions with chain N, Hydrophobic interactions: O:L.50, O:F.51, O:F.110, O:F.110, O:I.113 Hydrogen bonds: O:V.54, O:Q.98 Salt bridges: O:R.53, O:R.102, N:H.90 pi-Stacking: O:H.67 Metal complexes: O:H.99 HEM.32: 19 residues within 4Å: Chain M: H.89, Q.93 Chain P: S.47, L.50, F.51, N.53, V.54, H.67, R.70, V.71, L.75, L.95, Q.98, H.99, R.102, Y.109, F.110, M.113 Ligands: HEM.26 13 PLIP interactions: 11 interactions with chain P, 2 interactions with chain M, Hydrophobic interactions: P:F.51, P:F.51, P:L.95, P:Y.109, P:F.110, P:F.110, P:M.113 Hydrogen bonds: P:V.54, M:Q.93 Salt bridges: P:R.102, M:H.89 pi-Stacking: P:H.67 Metal complexes: P:H.99 HEM.35: 19 residues within 4Å: Chain Q: L.45, F.46, S.48, V.49, H.62, R.65, V.66, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain T: H.94, Q.98 Ligands: HEM.40 21 PLIP interactions: 19 interactions with chain Q, 2 interactions with chain T, Hydrophobic interactions: Q:L.45, Q:F.46, Q:F.46, Q:V.49, Q:L.70, Q:L.99, Q:N.103, Q:F.104, Q:F.104, Q:F.104, Q:F.107, Q:F.107, Q:I.135, Q:I.139 Hydrogen bonds: Q:S.48, T:Q.98 Water bridges: Q:S.48 Salt bridges: Q:R.65, T:H.94 pi-Stacking: Q:H.62 Metal complexes: Q:H.94 HEM.36: 18 residues within 4Å: Chain R: M.46, F.47, R.49, V.50, H.63, R.66, V.67, L.71, L.91, Q.94, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain S: H.94 14 PLIP interactions: 13 interactions with chain R, 1 interactions with chain S, Hydrophobic interactions: R:F.47, R:V.67, R:L.91, R:V.100, R:Q.104, R:Y.105, R:V.108, R:I.141 Hydrogen bonds: R:R.49, R:V.50, R:R.98 Salt bridges: R:R.49, S:H.94 Metal complexes: R:H.95 HEM.38: 20 residues within 4Å: Chain R: H.90, Q.94 Chain S: L.50, F.51, R.53, V.54, H.67, R.70, V.71, L.75, Q.98, H.99, R.102, V.105, G.109, F.110, I.113, T.141, M.144 Ligands: OXY.39 19 PLIP interactions: 17 interactions with chain S, 2 interactions with chain R, Hydrophobic interactions: S:L.50, S:F.51, S:F.51, S:V.71, S:L.75, S:R.102, S:F.110, S:F.110, S:I.113, S:T.141 Hydrogen bonds: S:Q.98, R:Q.94 Water bridges: S:R.53 Salt bridges: S:R.53, S:H.67, S:R.70, S:R.102, R:H.90 Metal complexes: S:H.99 HEM.40: 17 residues within 4Å: Chain Q: H.89, Q.93 Chain T: F.51, N.53, V.54, H.67, R.70, V.71, Q.98, H.99, R.102, L.105, Y.109, F.110, M.113 Ligands: HEM.35, OXY.41 17 PLIP interactions: 15 interactions with chain T, 2 interactions with chain Q, Hydrophobic interactions: T:F.51, T:F.51, T:V.71, T:L.105, T:L.105, T:Y.109, T:F.110, T:F.110, T:F.110, T:F.110, T:M.113 Hydrogen bonds: T:N.53, Q:Q.93 Salt bridges: T:R.102, Q:H.89 pi-Stacking: T:H.67 Metal complexes: T:H.99 HEM.42: 18 residues within 4Å: Chain U: L.45, F.46, S.48, H.62, R.65, G.69, L.70, H.94, R.97, L.99, N.103, F.104, F.107, I.135, I.139 Chain X: H.94, Q.98 Ligands: HEM.48 20 PLIP interactions: 17 interactions with chain U, 3 interactions with chain X, Hydrophobic interactions: U:F.46, U:F.46, U:L.70, U:L.99, U:N.103, U:F.104, U:F.104, U:F.104, U:F.107, U:F.107, U:F.107, U:I.135, U:I.139 Hydrogen bonds: U:R.65, X:Q.98 Salt bridges: U:R.65, X:H.94, X:H.94 pi-Stacking: U:H.62 Metal complexes: U:H.94 HEM.43: 19 residues within 4Å: Chain V: M.46, F.47, R.49, V.50, H.63, R.66, V.67, G.70, L.71, L.91, H.95, R.98, V.100, Q.104, Y.105, V.108, I.141 Chain W: H.94 Ligands: OXY.44 16 PLIP interactions: 1 interactions with chain W, 15 interactions with chain V, Salt bridges: W:H.94, V:R.98 Hydrophobic interactions: V:F.47, V:F.47, V:L.71, V:L.71, V:L.91, V:L.91, V:Q.104, V:Y.105, V:Y.105, V:V.108, V:I.141 Hydrogen bonds: V:R.98 pi-Stacking: V:H.63 Metal complexes: V:H.95 HEM.46: 18 residues within 4Å: Chain V: H.90 Chain W: L.50, F.51, R.53, V.54, H.67, R.70, V.71, G.74, L.75, Q.98, H.99, R.102, G.109, F.110, I.113, M.144 Ligands: OXY.47 12 PLIP interactions: 11 interactions with chain W, 1 interactions with chain V, Hydrophobic interactions: W:L.50, W:F.51, W:F.110, W:F.110, W:I.113 Hydrogen bonds: W:V.54, W:Q.98 Salt bridges: W:R.53, W:R.102, V:H.90 pi-Stacking: W:H.67 Metal complexes: W:H.99 HEM.48: 19 residues within 4Å: Chain U: H.89, Q.93 Chain X: S.47, L.50, F.51, N.53, V.54, H.67, R.70, V.71, L.75, L.95, Q.98, H.99, R.102, Y.109, F.110, M.113 Ligands: HEM.42 14 PLIP interactions: 2 interactions with chain U, 12 interactions with chain X, Hydrogen bonds: U:Q.93, X:V.54 Salt bridges: U:H.89, X:R.102 Hydrophobic interactions: X:F.51, X:F.51, X:L.95, X:Y.109, X:F.110, X:F.110, X:M.113 pi-Stacking: X:H.67, X:H.67 Metal complexes: X:H.99

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain B: N.106, E.109, D.135 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.109, B:E.109, B:D.135, H2O.1 CA.13: 4 residues within 4Å: Chain F: N.106, E.109, Q.131, D.135 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.109, F:D.135 CA.21: 3 residues within 4Å: Chain J: N.106, E.109, D.135 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.109, J:E.109, J:D.135, H2O.6 CA.29: 4 residues within 4Å: Chain N: N.106, E.109, Q.131, D.135 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:E.109, N:D.135 CA.37: 3 residues within 4Å: Chain R: N.106, E.109, D.135 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.109, R:E.109, R:D.135, H2O.10 CA.45: 4 residues within 4Å: Chain V: N.106, E.109, Q.131, D.135 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:E.109, V:D.135

12 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 6 residues within 4Å: Chain C: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.67 OXY.9: 6 residues within 4Å: Chain D: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) OXY.12: 6 residues within 4Å: Chain F: W.33, F.47, H.63, V.67, H.95 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.63 OXY.15: 5 residues within 4Å: Chain G: F.37, F.51, H.67, V.71 Ligands: HEM.14 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.67 OXY.23: 6 residues within 4Å: Chain K: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.22 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.67 OXY.25: 6 residues within 4Å: Chain L: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.24 No protein-ligand interaction detected (PLIP) OXY.28: 6 residues within 4Å: Chain N: W.33, F.47, H.63, V.67, H.95 Ligands: HEM.27 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.63 OXY.31: 5 residues within 4Å: Chain O: F.37, F.51, H.67, V.71 Ligands: HEM.30 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:H.67 OXY.39: 6 residues within 4Å: Chain S: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.38 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:H.67 OXY.41: 6 residues within 4Å: Chain T: F.37, F.51, H.67, V.71, H.99 Ligands: HEM.40 No protein-ligand interaction detected (PLIP) OXY.44: 6 residues within 4Å: Chain V: W.33, F.47, H.63, V.67, H.95 Ligands: HEM.43 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:H.63 OXY.47: 5 residues within 4Å: Chain W: F.37, F.51, H.67, V.71 Ligands: HEM.46 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:H.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numoto, N. et al., Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobio. (2022)

Release Date

2022-05-18

Peptides

Extracellular A1 globin: AEIMQU
Extracellular A2 globin: BFJNRV
Extracellular B2 globin: CGKOSW
Extracellular B1 globin: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
A

M
E

Q
A

U
E

B
B

F
F

J
B

N
F

R
B

V
F

C
C

G
G

K
C

O
G

S
C

W
G

D
D

H
H

L
D

P
H

T
D

X
H

Extracellular A1 globin

Extracellular A2 globin

Extracellular B2 globin

Extracellular B1 globin

Related Entries With Identical Sequence